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Does regulation in the genome use collective behavior, similar to the way the brain or deep neural networks operate? Here I make the case for why having a genomic network capable of a high level of computation would be strongly selected for, and suggest how it might arise from biochemical processes that succeed in regulating in a collective manner, very different than the usual way we think about genetic regulation., Comment: 5 pages, 0 figures

Cosmological boundary conditions for particles and fields are often discussed as a Cauchy problem, in which configurations and conjugate momenta are specified on an "initial" time slice. But this is not the only way to specify boundary conditions, and indeed in action-principle formulations we often specify configurations at two times and consider trajectories joining them. Here, we consider a classical system of particles interacting with short range two body interactions, with boundary conditions on the particles' positions for an initial and a final time. For a large number of particles that are randomly arranged into a dilute gas, we find that a typical system trajectory will spontaneously collapse into a small region of space, close to the maximum density that is obtainable, before expanding out again. If generalizable, this has important implications for the cosmological arrow of time, potentially allowing a scenario in which both boundary conditions are generic and also a low-entropy state "initial" state of the universe naturally occurs., Comment: 12 pages, 7 figures

In the past several years, observational entropy has been developed as both a (time-dependent) quantum generalization of Boltzmann entropy, and as a rather general framework to encompass classical and quantum equilibrium and non-equilibrium coarse-grained entropy. In this paper we review the construction, interpretation, most important properties, and some applications of this framework. The treatment is self-contained and relatively pedagogical, aimed at a broad class of researchers., Comment: Review of recent developments in observational entropy in isolated systems. 8+4 pages, 3 figures, 1 table

In this paper, we investigate and compare two well-developed definitions of entropy relevant for describing the dynamics of isolated quantum systems: bipartite entanglement entropy and observational entropy. In a model system of interacting particles in a one-dimensional lattice, we numerically solve for the full quantum behavior of the system. We characterize the fluctuations, and find the maximal, minimal, and typical entropy of each type that the system can eventually attain through its evolution. While both entropies are low for some "special" configurations and high for more "generic" ones, there are several fundamental differences in their behavior. Observational entropy behaves in accord with classical Boltzmann entropy (e.g. equilibrium is a condition of near-maximal entropy and uniformly distributed particles, and minimal entropy is a very compact configuration). Entanglement entropy is rather different: minimal entropy "empties out" one partition while maximal entropy apportions the particles between the partitions, and neither is typical. Beyond these qualitative results, we characterize both entropies and their fluctuations in some detail as they depend on temperature, particle number, and box size., Comment: Additional comments are made in the caption of figure 10 (a). Equation 7 and a brief description are added in relation to figure 4

We develop the framework of classical Observational entropy, which is a mathematically rigorous and precise framework for non-equilibrium thermodynamics, explicitly defined in terms of a set of observables. Observational entropy can be seen as a generalization of Boltzmann entropy to systems with indeterminate initial conditions, and describes the knowledge achievable about the system by a macroscopic observer with limited measurement capabilities; it becomes Gibbs entropy in the limit of perfectly fine-grained measurements. This quantity, while previously mentioned in the literature, has been investigated in detail only in the quantum case. We describe this framework reasonably pedagogically, then show that in this framework, certain choices of coarse-graining lead to an entropy that is well-defined out of equilibrium, additive on independent systems, and that grows towards thermodynamic entropy as the system reaches equilibrium, even for systems that are genuinely isolated. Choosing certain macroscopic regions, this dynamical thermodynamic entropy measures how close these regions are to thermal equilibrium. We also show that in the given formalism, the correspondence between classical entropy (defined on classical phase space) and quantum entropy (defined on Hilbert space) becomes surprisingly direct and transparent, while manifesting differences stemming from non-commutativity of coarse-grainings and from non-existence of a direct classical analogue of quantum energy eigenstates., Comment: 15+6 pages, 6 figures, 1 table. v2: literature review extended, added a discussion of Observational entropy with local energy coarse-graining (FOE) and its properties, added physical/operational interpretations of both FOE and S_xE. Comments and questions are very much welcome

The evolution of the genome has led to very sophisticated and complex regulation. Because of the abundance of non-coding RNA (ncRNA) in the cell, different species will promiscuously associate with each other, suggesting collective dynamics similar to artificial neural networks. Here we present a simple mechanism allowing ncRNA to perform computations equivalent to neural network algorithms such as Boltzmann machines and the Hopfield model. The quantities analogous to the neural couplings are the equilibrium constants between different RNA species. The relatively rapid equilibration of RNA binding and unbinding is regulated by a slower process that degrades and creates new RNA. The model requires that the creation rate for each species be an increasing function of the ratio of total to unbound RNA. Similar mechanisms have already been found to exist experimentally for ncRNA regulation. With the overall concentration of RNA regulated, equilibrium constants can be chosen to store many different patterns, or many different input-output relations. The network is also quite insensitive to random mutations in equilibrium constants. Therefore one expects that this kind of mechanism will have a much higher mutation rate than ones typically regarded as being under evolutionary constraint., Comment: 18 pages, 10 figures

We investigate the detailed properties of Observational entropy, introduced by \v{S}afr\'{a}nek et al. [Phys. Rev. A 99, 010101 (2019)] as a generalization of Boltzmann entropy to quantum mechanics. This quantity can involve multiple coarse-grainings, even those that do not commute with each other, without losing any of its properties. It is well-defined out of equilibrium, and for some coarse-grainings it generically rises to the correct thermodynamic value even in a genuinely isolated quantum system. The quantity contains several other entropy definitions as special cases, it has interesting information-theoretic interpretations, and mathematical properties -- such as extensivity and upper and lower bounds -- suitable for an entropy. Here we describe and provide proofs for many of its properties, discuss its interpretation and connection to other quantities, and provide numerous simulations and analytic arguments supporting the claims of its relationship to thermodynamic entropy. This quantity may thus provide a clear and well-defined foundation on which to build a satisfactory understanding of the second thermodynamical law in quantum mechanics., Comment: 24+17 pages, 9 figures, v2: added some new results and figures, extended section on comparison with other entropy measures

We extend classical coarse-grained entropy, commonly used in many branches of physics, to the quantum realm. We find two coarse-grainings, one using measurements of local particle numbers and then total energy, and the second using local energy measurements, which lead to an entropy that is defined outside of equilibrium, is in accord with the thermodynamic entropy for equilibrium systems, and reaches the thermodynamic entropy in the long-time limit, even in genuinely isolated quantum systems. This answers the long-standing conceptual problem, as to which entropy is relevant for the formulation of the second thermodynamic law in closed quantum systems. This entropy could be in principle measured, especially now that experiments on such systems are becoming feasible., Comment: 6 pages, 2 figures, v2: extended motivation, added more detailed interpretation, added more properties, v3: minor changes in references

A large $\mu^-$ polarization was achieved in muonic Bi atoms with the help of the strong hyperfine field in a polarized nuclear target. Using $^{209}$Bi nuclei polarized to ($59\pm9$)% in ferromagnetic BiMn, we observed a $\mu$-$e$ decay asymmetry of ($13.1\pm3.9$)%, which gives $\mu^-$ polarization per nuclear polarization equal to $-1.07\pm 0.35$. This value is almost consistent with $-0.792$ calculated for nuclei with spin $I= \frac{9}{2}$ and a positive magnetic moment under the assumption that the hyperfine interaction becomes effective in the lowest muonic states., Comment: Corrected version of original paper, 4 pages, 2 figures, corrections indicated by red

The majority of mammalian genomic transcripts do not directly code for proteins and it is currently believed that most of these are not under evolutionary constraint. However given the abundance non-coding RNA (ncRNA) and its strong affinity for inter-RNA binding, these molecules have the potential to regulate proteins in a highly distributed way, similar to artificial neural networks. We explore this analogy by devising a simple architecture for a biochemical network that can function as an associative memory. We show that the steady state solution for this chemical network has the same structure as an associative memory neural network model. By allowing the choice of equilibrium constants between different ncRNA species, the concentration of unbound ncRNA can be made to follow any pattern and many patterns can be stored simultaneously. The model is studied numerically and within certain parameter regimes it functions as predicted. Even if the starting concentration pattern is quite different, it is shown to converge to the original pattern most of the time. The network is also robust to mutations in equilibrium constants. This calls into question the criteria for deciding if a sequence is under evolutionary constraint., Comment: 7 pages, 2 figures

Background: The rate \lambda_pp\mu\ characterizes the formation of pp\mu\ molecules in collisions of muonic p\mu\ atoms with hydrogen. In measurements of the basic weak muon capture reaction on the proton to determine the pseudoscalar coupling g_P, capture occurs from both atomic and molecular states. Thus knowledge of \lambda_pp\mu\ is required for a correct interpretation of these experiments. Purpose: Recently the MuCap experiment has measured the capture rate \Lambda_S from the singlet p\mu\ atom, employing a low density active target to suppress pp\mu\ formation (PRL 110, 12504 (2013)). Nevertheless, given the unprecedented precision of this experiment, the existing experimental knowledge in \lambda_pp\mu\ had to be improved. Method: The MuCap experiment derived the weak capture rate from the muon disappearance rate in ultra-pure hydrogen. By doping the hydrogen with 20 ppm of argon, a competing process to pp\mu\ formation was introduced, which allowed the extraction of \lambda_pp\mu\ from the observed time distribution of decay electrons. Results: The pp\mu\ formation rate was measured as \lambda_pp\mu = (2.01 +- 0.06(stat) +- 0.03(sys)) 10^6 s^-1. This result updates the \lambda_pp\mu\ value used in the above mentioned MuCap publication. Conclusions: The 2.5x higher precision compared to earlier experiments and the fact that the measurement was performed at nearly identical conditions to the main data taking, reduces the uncertainty induced by \lambda_pp\mu\ to a minor contribution to the overall uncertainty of \Lambda_S and g_P, as determined in MuCap. Our final value for \lambda_pp\mu\ shifts \Lambda_S and g_P by less than one tenth of their respective uncertainties compared to our results published earlier., Comment: 12 pages, 6 figures, to be submitted to Phys. Rev. C

We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into account the equilibrium constants between bound and unbound states. By including the pair-wise binding of the many RNA species, the network becomes highly interconnected and shows different properties than the usual type of genetic network. It shows much more robustness to mutation, and also rapid evolutionary adaptation in an environment that oscillates in time. This provides a possible explanation for the weak evolutionary constraints seen in much of the non-coding RNA that has been studied., Comment: 9 pages, 4 figures

The Michel parameter xi" has been determined from a measurement of the longitudinal polarization of positrons emitted in the decay of polarized and depolarized muons. The result, xi" = 0.981 +- 0.045stat +- 0.003syst, is consistent with the Standard Model prediction of unity, and provides an order of magnitude improvement in the relative precision of this parameter. This value sets new constraints on exotic couplings beyond the dominant V-A description of the leptonic weak interaction., Comment: 15 pages, 16 figures, 3 tables; submitted to Phys. Rev. D

We analyze experimental observations of microtubules undergoing small fluctuations about a "balance point" when mixed in solution of two different kinesin motor proteins, KLP61F and Ncd. It has been proposed that the microtubule movement is due to stochastic variations in the densities of the two species of motor proteins. We test this hypothesis here by showing how it maps onto a one-dimensional random walk in a random environment. Our estimate of the amplitude of the fluctuations agrees with experimental observations. We point out that there is an initial transient in the position of the microtubule where it will typically move of order its own length. We compare the physics of this gliding assay to a recent theory of the role of antagonistic motors on restricting interpolar microtubule sliding of a cell's mitotic spindle during prometaphase. It is concluded that randomly positioned antagonistic motors can restrict relative movement of microtubules, however they do so imperfectly. A variation in motor concentrations is also analyzed and shown to lead to greater control of spindle length., Comment: 13 pages, 7 figures

Biophysics is a subject that is spread over many disciplines and transcends the skills and knowledge of the individual student. This makes it challenging both to teach and to learn. Educational materials are described to aid in teaching undergraduates biophysics in an interdisciplinary manner. Projects have been devised on topics that range from x-ray diffraction to the Hodgkin Huxley equations. They are team-based and encourage collaboration. The projects make extensive use of software written in Python/Scipy which can be modified to explore a large range of possible phenomena. The software can also be used in lectures and in the teaching of more traditional biophysics courses., Comment: 22 pages, 13 figures

A device is investigated that continuously and directly converts light into mechanical energy, using polymers and photodissociation. A polymer brush tethered to a surface, is brought into contact with a parallel plate a small distance above it that contains reaction sites where photodissociation of bound polymer and light can occur. Under the appropriate conditions, the collective effect of these polymers is to apply a force parallel to the plates, converting incoming light into mechanical work. Numerical work is carried out to understand this effect, a three dimensional Langevin simulation, solution to the Fokker Planck equation, and a one dimensional Monte Carlo simulation. Theoretical analysis of the Fokker Planck equation is used to study a model where equilibration of the unbound state occurs and equilibration to a metastable equilibrium is achieved in the bound state. It is shown that the work per cycle can be made much larger than the thermal energy but at the expense of requiring a greatly diminished photodissociation rate. Parameters are discussed in order optimize mechanical energy conversion., Comment: 11 pages, 8 figures

The MuCap experiment at the Paul Scherrer Institute has measured the rate L_S of muon capture from the singlet state of the muonic hydrogen atom to a precision of 1%. A muon beam was stopped in a time projection chamber filled with 10-bar, ultra-pure hydrogen gas. Cylindrical wire chambers and a segmented scintillator barrel detected electrons from muon decay. L_S is determined from the difference between the mu- disappearance rate in hydrogen and the free muon decay rate. The result is based on the analysis of 1.2 10^10 mu- decays, from which we extract the capture rate L_S = (714.9 +- 5.4(stat) +- 5.1(syst)) s^-1 and derive the proton's pseudoscalar coupling g_P(q^2_0 = -0.88 m^2_mu) = 8.06 +- 0.55., Comment: Updated figure 1 and small changes in wording to match published version

A microscopic understanding of the thermodynamic entropy in quantum systems has been a mystery ever since the invention of quantum mechanics. In classical physics, this entropy is believed to be the logarithm of the volume of phase space accessible to an isolated system [1]. There is no quantum mechanical analog to this. Instead, Von Neumann's hypothesis for the entropy [2] is most widely used. However this gives zero for systems with a known wave function, that is a pure state. This is because it measures the lack of information about the system rather than the flow of heat as obtained from thermodynamic experiments. Many arguments attempt to sidestep these issues by considering the system of interest coupled to a large external one, unlike the classical case where Boltzmann's approach for isolated systems is far more satisfactory. With new experimental techniques, probing the quantum nature of thermalization is now possible [3, 4]. Here, using recent advances in our understanding of quantum thermalization [5-10] we show how to obtain the entropy as is measured from thermodynamic experiments, solely from the self-entanglement of the wavefunction, and find strong numerical evidence that the two are in agreement for non-integrable systems. It is striking that this entropy, which is closely related to the concept of heat, and generally thought of as microscopic chaotic motion, can be determined for systems in energy eigenstates which are stationary in time and therefore not chaotic, but instead have a very complex spatial dependence., Comment: Manuscript is 5 pages, 2 figures, plus supplementary materials of 8 pages and 5 figures

We analyze the nonlinear waves that propagate on a microtubule that is tethered at its minus end due to kinesin walking on it, as is seen during the fluid mixing caused by cytoplasmic streaming in Drosophila oocytes.The model we use assumes that the microtubule can be modeled as an elastic string in a viscous medium. The effect of the kinesin is to apply a force tangential to the microtubule and we also consider the addition of a uniform cytoplasmic velocity field. We show that travelling wave solutions exist and analyze their properties. There exist scale invariant families of solutions and solutions can exist that are flat or helical. The relationship between the period and wavelength is obtained by both analytic and numerical means. Numerical implementation of the equation of motion verifies our analytical predictions., Comment: 14 pages, 6 figures

Large scale motion of cytoplasm called cytoplasmic streaming occurs in some large eukaryotic cells to stir the cell's constituents. In Drosophila oocytes, microtubules have been observed to undergo undulating motion, curving to form travelling waves during cytoplasmic streaming. Here we show that this wave-like motion can be understood physically as due to the hydrodynamic drag of streaming impellers attached to kinesin motors moving toward the plus-ends of microtubules whose minus ends are anchored to the cell cortex. The tangential forces applied to such microtubules by kinesin give rise to bending and leads to chiral symmetry breaking causing the microtubules to propagate long travelling waves. The waves are reminiscent of those seen in flagellar motion but of a much longer time scale and by a different physical mechanism. We show how kinesin movement can produce a bulk flow of cytoplasm surrounding a microtubule with the range of flow greatly enhanced by the effect of hydrodynamic coupling between impellers. That is, a relatively small number of motors can move a large amount of fluid. The chaotic nature of the fluid motion of cytoplasm caused by kinesin movement along constantly changing microtubule trajectories is important as it greatly enhances the efficiency of mixing. Existing data on in vitro microtubule gliding assays also show this chiral instability in two dimensions and an analysis of this gives quantitative estimates for the forces exerted by motors and the drag coefficient., Comment: 7 pages, 3 figures

We study self avoiding random walks in an environment where sites are excluded randomly, in two and three dimensions. For a single polymer chain, we study the statistics of the time averaged monomer density and show that these are well described by multifractal statistics. This is true even far from the percolation transition of the disordered medium. We investigate solutions of chains in a disordered environment and show that the statistics cease to be multifractal beyond the screening length of the solution., Comment: 5 pages, 6 figures

The statistical mechanics of a linear non-interacting polymer chain with a large number of monomers is considered with fixed angular momentum. The radius of gyration for a linear polymer is derived exactly by functional integration. This result is then compared to simulations done with a large number of non-interacting rigid links at fixed angular momentum. The simulation agrees with the theory up to finite size corrections. The simulations are also used to investigate the anisotropic nature of a spinning polymer. We find universal scaling of the polymer size along the direction of the angular momentum, as a function of rescaled angular momentum., Comment: 7 pages, 3 figures

In a number of experimental situations, single polymer molecules can be suspended in a vacuum. Here collisions between such molecules are considered. The limit of high collision velocity is investigated numerically for a variety of conditions. The distribution of contact times, scattering angles, and final velocities are analyzed. In this limit, self avoiding chains are found to become highly stretched as they collide with each other, and have a distribution of scattering times that depends on the scattering angle. The velocity of the molecules after the collisions is similar to predictions of a model assuming thermal equilibration of molecules during the collision. The most important difference is a significant subset of molecules that inelastically scatter but do not substantially change direction., Comment: 7 pages, 6 figures

The dynamics of flexible polymer molecules are often assumed to be governed by hydrodynamics of the solvent. However there is considerable evidence that internal dissipation of a polymer contributes as well. Here we investigate the dynamics of a single chain in the absence of solvent to characterize the nature of this internal friction. We model the chains as freely hinged but with localized bond angles and 3-fold symmetric dihedral angles. We show that the damping is close but not identical to Kelvin damping, which depends on the first temporal and second spatial derivative of monomer position. With no internal potential between monomers, the magnitude of the damping is small for long wavelengths and weakly damped oscillatory time dependent behavior is seen for a large range of spatial modes. When the size of the internal potential is increased, such oscillations persist, but the damping becomes larger. However underdamped motion is present even with quite strong dihedral barriers for long enough wavelengths., Comment: 6 pages, 8 figures

It is argued that a typical many body energy eigenstate has a well defined thermodynamic entropy and that individual eigenstates possess thermodynamic characteristics analogous to those of generic isolated systems. We examine large systems with eigenstate energies equivalent to finite temperatures. When quasi-static evolution of a system is adiabatic (in the quantum mechanical sense), two coupled subsystems can transfer heat from one subsystem to another yet remain in an energy eigenstate. To explicitly construct the entropy from the wave function, degrees of freedom are divided into two unequal parts. It is argued that the entanglement entropy between these two subsystems is the thermodynamic entropy per degree of freedom for the smaller subsystem. This is done by tracing over the larger subsystem to obtain a density matrix, and calculating the diagonal and off-diagonal contributions to the entanglement entropy., Comment: 18 pages

We study stress relaxation in bi-disperse entangled polymer solutions. Shorter chains embedded in a majority of longer ones are known to be oriented by coupling to them. We analyze the mechanism for this both by computer simulation and theoretically. We show that the results can be understood in terms of stress fluctuations in a polymer melt and chain screening. Stress fluctuations are frozen on the relaxation time of the longer chains, and these will induce strong orientational couplings in the shorter chains., Comment: 5 pages, 2 figures

The statistical mechanics of a non-interacting polymer chain in the limit of a large number of monomers is considered when the total angular momentum, L, is fixed. The radius of gyration for a ring polymer in this situation is derived exactly in closed form by functional integration techniques. Even when L = 0 the radius of gyration differs from that of a random walk by a prefactor of order unity. The dependence on L is discussed qualitatively and the large L limit can be understood by physical arguments., Comment: 9 pages, 2 figures

We show for the Ising model that is possible construct a discrete time stochastic model analogous to the Langevin equation that incorporates an arbitrary amount of damping. It is shown to give the correct equilibrium statistics and is then used to investigate nonequilibrium phenomena, in particular, magnetic avalanches. The value of damping can greatly alter the shape of hysteresis loops, and for small damping and high disorder, the morphology of large avalanches can be drastically effected. Small damping also alters the size distribution of avalanches at criticality., Comment: 8 pages, 8 figures, 2 column

In a variety of situations, isolated polymer molecules are found in a vacuum and here we examine their properties. Angular momentum conservation is shown to significantly alter the average size of a chain and its conservation is only broken slowly by thermal radiation. The time autocorrelation for monomer position oscillates with a characteristic time proportional to chain length. The oscillations and damping are analyzed in detail. Short range repulsive interactions suppress oscillations and speed up relaxation but stretched chains still show damped oscillatory time correlations., Comment: 4 pages, 3 figures, two column format

The rate of nuclear muon capture by the proton has been measured using a new experimental technique based on a time projection chamber operating in ultra-clean, deuterium-depleted hydrogen gas at 1 MPa pressure. The capture rate was obtained from the difference between the measured $\mu^-$ disappearance rate in hydrogen and the world average for the $\mu^+$ decay rate. The target's low gas density of 1% compared to liquid hydrogen is key to avoiding uncertainties that arise from the formation of muonic molecules. The capture rate from the hyperfine singlet ground state of the $\mu p$ atom is measured to be $\Lambda_S=725.0 \pm 17.4 s^{-1}$, from which the induced pseudoscalar coupling of the nucleon, $g_P(q^2=-0.88 m_\mu^2)=7.3 \pm 1.1$, is extracted. This result is consistent with theoretical predictions for $g_P$ that are based on the approximate chiral symmetry of QCD., Comment: submitted to Phys.Rev.Lett

Beautiful theories of magnetic hysteresis based on random microscopic disorder have been developed over the past ten years. Our goal was to directly compare these theories with precise experiments. We first developed and then applied coherent x-ray speckle metrology to a series of thin multilayer perpendicular magnetic materials. To directly observe the effects of disorder, we deliberately introduced increasing degrees of disorder into our films. We used coherent x-rays to generate highly speckled magnetic scattering patterns. The apparently random arrangement of the speckles is due to the exact configuration of the magnetic domains in the sample. In effect, each speckle pattern acts as a unique fingerprint for the magnetic domain configuration. Small changes in the domain structure change the speckles, and comparison of the different speckle patterns provides a quantitative determination of how much the domain structure has changed. How is the magnetic domain configuration at one point on the major hysteresis loop related to the configurations at the same point on the loop during subsequent cycles? The microscopic return-point memory(RPM) is partial and imperfect in the disordered samples, and completely absent when the disorder was not present. We found the complementary-point memory(CPM) is also partial and imperfect in the disordered samples and completely absent when the disorder was not present. We found that the RPM is always a little larger than the CPM. We also studied the correlations between the domains within a single ascending or descending loop. We developed new theoretical models that do fit our experiments., Comment: 26 pages, 25 figures, Accepted by Physical Review B 01/25/07

In many magnetic materials, spin dynamics at short times are dominated by precessional motion as damping is relatively small. In the limit of no damping and no thermal noise, we show that for a large enough initial instability, an avalanche can transition to an ergodic phase where the state is equivalent to one at finite temperature, often above that for ferromagnetic ordering. This dynamical nucleation phenomenon is analyzed theoretically. For small finite damping the high temperature growth front becomes spread out over a large region. The implications for real materials are discussed., Comment: 4 pages 2 figures

Magnetic thin films exhibit a strong variation in properties depending on their degree of disorder. Recent coherent x-ray speckle experiments on magnetic films have measured the loss of correlation between configurations at opposite fields and at the same field, upon repeated field cycling. We perform finite temperature numerical simulations on these systems that provide a comprehensive explanation for the experimental results. The simulations demonstrate, in accordance with experiments, that the memory of configurations increases with film disorder. We find that non-trivial microscopic differences exist between the zero field spin configuration obtained by starting from a large positive field and the zero field configuration starting at a large negative field. This seemingly paradoxical beahvior is due to the nature of the vector spin dynamics and is also seen in the experiments. For low disorder, there is an instability which causes the spontaneous growth of line-like domains at a critical field, also in accord with experiments. It is this unstable growth, which is highly sensitive to thermal noise, that is responsible for the small correlation between patterns under repeated cycling. The domain patterns, hysteresis loops, and memory properties of our simulated systems match remarkably well with the real experimental systems., Comment: 12 pages, 10 figures Added comparison of results with cond-mat/0412461 and some more discussion

We have set limits on contributions of scalar interactions to nuclear beta decay. A magneto-optical trap (MOT) provides a localized source of atoms suspended in space, so the low-energy recoiling nuclei can freely escape and be detected in coincidence with the beta. This allows reconstruction of the neutrino momentum, and the measurement of the beta-neutrino correlation, in a more direct fashion than previously possible. The beta-neutrino correlation parameter of the 0+ to 0+ pure Fermi decay of 38mK is $\tilde{a}$=0.9981+-0.0030+-0.0037, consistent with the standard model prediction a=1., Comment: 4 pages, 3 figures, accepted by Phys. Rev. Lett., centroid changed

Using coherent x-ray speckle metrology, we have measured the influence of disorder on major loop return point memory (RPM) and complementary point memory (CPM) for a series of perpendicular anisotropy Co/Pt multilayer films. In the low disorder limit, the domain structures show no memory with field cycling--no RPM and no CPM. With increasing disorder, we observe the onset and the saturation of both the RPM and the CPM. These results provide the first direct ensemble-sensitive experimental study of the effects of varying disorder on microscopic magnetic memory and are compared against the predictions of existing theories., Comment: 4 pages, 4 figures. Accepted for publication in Physical Review Letters in Nov. 2004

We study the behavior of self avoiding polymers in a background of vertically aligned rods that are either frozen into random positions or free to move horizontally. We find that in both cases the polymer chains are highly elongated, with vertical and horizontal size exponents that differ by a factor of 3. Though these results are different than previous predictions, our results are confirmed by detailed computer simulations., Comment: 4 pages, 4 figures

We predict two new physical effects in arrays of single-domain nanomagnets by performing simulations using a realistic model Hamiltonian and physical parameters. First, we find hysteretic multicycles for such nanomagnets. The simulation uses continuous spin dynamics through the Landau-Lifshitz-Gilbert (LLG) equation. In some regions of parameter space, the probability of finding a multicycle is as high as ~0.6. We find that systems with larger and more anisotropic nanomagnets tend to display more multicycles. This result demonstrates the importance of disorder and frustration for multicycle behavior. We also show that there is a fundamental difference between the more realistic vector LLG equation and scalar models of hysteresis, such as Ising models. In the latter case, spin and external field inversion symmetry is obeyed but in the former it is destroyed by the dynamics, with important experimental implications., Comment: 7 pages, 2 figures

The ability of oligonucleotide microarrays to measure gene expression has been hindered by an imperfect understanding of the relationship between input RNA concentrations and output signals. We argue that this relationship can be understood based on the underlying statistical mechanics of these devices. We present a model that includes the relevant interactions between the molecules. Our model for the first time accounts for partially zippered probe-target hybrids in a physically realistic manner, and also includes target-target binding in solution. Large segments of the target molecules are not bound to the probes, often in an asymmetric pattern, emphasizing the importance of modeling zippering properly. The resultant fit between the model and training data using optimized parameters is excellent, and it also does well at predicting test data., Comment: 4 pages, 4 figures

We describe a new class of systems exhibiting return point memory (RPM) that are different from those discussed before in the context of ferromagnets. We show numerically that one dimensional random Ising antiferromagnets have RPM, when configurations evolve from a large field. However, RPM is violated when started from some stable configurations at finite field unlike in the ferromagnetic case. This implies that the standard approach to understanding ferromagnetic RPM systems will fail for this case. We also demonstrate RPM with a set of variables that keep track of spin flips at each site. Conventional RPM for the spin configuration is a projection of this result, suggesting that spin flip variables might be a more fundamental representation of the dynamics. We also present a mapping that embeds the antiferromagnetic chain in a two dimensional ferromagnetic model, and prove RPM for spin exchange dynamics in the interior of the chain with this mapping.

We examine numerically the full spatio-temporal correlation functions for all hydrodynamic quantities for the random collision model introduced recently. The autocorrelation function of the heat current, through the Kubo formula, gives a thermal conductivity exponent of 1/3 in agreement with the analytical prediction and previous numerical work. Remarkably, this result depends crucially on the choice of boundary conditions: for periodic boundary conditions (as opposed to open boundary conditions with heat baths) the exponent is approximately 1/2. This is expected to be a generic feature of systems with singular transport coefficients. All primitive hydrodynamic quantities scale with the dynamic critical exponent predicted analytically., Comment: 7 pages, 11 figures

We study numerically the thermal conductivity coefficient $\kappa$ as a function of system length $L$ for several different quasi one dimensional models: classical gases of hard spheres with both longitudinal and transverse degrees of freedom. We introduce a model that is ergodic and highly chaotic but also conserves energy and momentum, and is very useful because it shows scaling even at small system sizes. We find that $\kappa \sim L^\alpha$ over more than two decades, with $\alpha$ very close to the analytical prediction of 1/3., Comment: 4 pages, 4 figures

The aim of the MuCap experiment is a 1% measurement of the singlet capture rate Lambda_S for the basic electro-weak reaction mu + p -> n + nu_mu. This observable is sensitive to the weak form-factors of the nucleon, in particular to the induced pseudoscalar coupling constant g_P. It will provide a rigorous test of theoretical predictions based on the Standard Model and effective theories of QCD. The present method is based on high precision lifetime measurements of mu^- in hydrogen gas and the comparison with the free mu^+ lifetime. The mu^- experiment will be performed in ultra-clean, deuterium-depleted H_2 gas at 10 bar. Low density compared to liquid H_2 is chosen to avoid uncertainties due to ppmu formation. A time projection chamber acts as a pure hydrogen active target. It defines the muon stop position in 3-D and detects rare background reactions. Decay electrons are tracked in cylindrical wire-chambers and a scintillator array covering 75% of 4 pi., Comment: Int. RIKEN Conf. on Muon Catalyzed Fusion and Related Exotic Atoms, April 2001, Shimoda, Japan, to be published in Hyperfine Interactions

Motivation: Microarray data has been recently been shown to be efficacious in distinguishing closely related cell types that often appear in the diagnosis of cancer. It is useful to determine the minimum number of genes needed to do such a diagnosis both for clinical use and to determine the importance of specific genes for cancer. Here a replication algorithm is used for this purpose. It evolves an ensemble of predictors, all using different combinations of genes to generate a set of optimal predictors. Results: We apply this method to the leukemia data of the Whitehead/MIT group that attempts to differentially diagnose two kinds of leukemia, and also to data of Khan et. al. to distinguish four different kinds of childhood cancers. In the latter case we were able to reduce the number of genes needed from 96 down to 15, while at the same time being able to perfectly classify all of their test data. Availability: http://stravinsky.ucsc.edu/josh/gesses/ Contact: josh@physics.ucsc.edu, Comment: 21 pages 8 figures latex