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Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of cell aggregates as bioink particles. Computer simulations based on Metropolis Monte Carlo (MMC) algorithms were successful in explaining and predicting the resulting stationary structures (corresponding to the lowest adhesion energy state). Here we present two alternatives to the MMC approach for modeling cellular motion and self-assembly: (1) a kinetic Monte Carlo (KMC), and (2) a cellular particle dynamics (CPD) method. Unlike MMC, both KMC and CPD methods are capable of simulating the dynamics of the cellular system in real time. In the KMC approach a transition rate is associated with possible rearrangements of the cellular system, and the corresponding time evolution is expressed in terms of these rates. In the CPD approach cells are modeled as interacting cellular particles (CPs) and the time evolution of the multicellular system is determined by integrating the equations of motion of all CPs. The KMC and CPD methods are tested and compared by simulating two experimentally well known phenomena: (1) cell-sorting within an aggregate formed by two types of cells with different adhesivities, and (2) fusion of two spherical aggregates of living cells., Comment: 11 pages, 7 figures; submitted to Phys Rev E

Often gaining insight into the functioning of biomolecular systems requires to follow their dynamics along a microscopic reaction coordinate (RC) on a macroscopic time scale, which is beyond the reach of current all atom molecular dynamics (MD) simulations. A practical approach to this inherently multiscale problem is to model the system as a fictitious overdamped Brownian particle that diffuses along the RC in the presence of an effective potential of mean force (PMF) due to the rest of the system. By employing the recently proposed FR method [I. Kosztin et al., J. of Chem. Phys. 124, 064106 (2006)], which requires only a small number of fast nonequilibrium MD simulations of the system in both forward and time reversed directions along the RC, we reconstruct the PMF: (1) of deca-alanine as a function of its end-to-end distance, and (2) that guides the motion of potassium ions through the gramicidin A channel. In both cases the computed PMFs are found to be in good agreement with previous results obtained by different methods. Our approach appears to be about one order of magnitude faster than the other PMF calculation methods and, in addition, it also provides the position dependent diffusion coefficient along the RC. Thus, the obtained PMF and diffusion coefficient can be used in a suitable stochastic model to estimate important characteristics of the studied systems, e.g., the mean folding time of the stretched deca-alanine and the mean diffusion time of the potassium ion through gramicidin A., Comment: 10 pages, 10 figures, submitted to PRE

We investigate the flow generated by a magnetic stirrer in cylindrical containers by optical observations, PIV measurements and particle and dye tracking methods. The tangential flow is that of an ideal vortex outside of a core, but inside downwelling occur with a strong jet in the very middle. In the core region dye patterns remain visible over minutes indicating a pure stirring and mixing property in this region. The results of quantitative measurements can be described by simple formulas in the investigated region of the stirring bar's rotation frequency. The tangential flow turns out to be dynamically similar to that of big atmospheric vortices like dust devils and tornadoes., Comment: Slightly revised version

The free motion of balls is investigated experimentally in continously stratified fluid in a finite container. The oscillation frequency is found to be very close to the local Brunt-Vaisala frequency. The effect of added mass proves to be practically negligible. The evolution of rear jets is demonstrated, and a kind of long term levitation is found. We show that the classical viscous drag would lead to a much stronger damping than observed in the experiment. This is interpreted as a consequence of the feedback from the previously excited internal waves following their reflection from the boundaries. A phenomenological equation with a modified drag term is proposed to obtain a qualitative agreement with the observations. We point out that the inclusion of a history term would lead further away from the observed data.

A general approach for calculating spectral and optical properties of pigment-protein complexes of known atomic structure is presented. The method, that combines molecular dynamics simulations, quantum chemistry calculations and statistical mechanical modeling, is demonstrated by calculating the absorption and circular dichroism spectra of the B800-B850 BChls of the LH2 antenna complex from Rs. molischianum at room temperature. The calculated spectra are found to be in good agreement with the available experimental results. The calculations reveal that the broadening of the B800 band is mainly caused by the interactions with the polar protein environment, while the broadening of the B850 band is due to the excitonic interactions. Since it contains no fitting parameters, in principle, the proposed method can be used to predict optical spectra of arbitrary pigment-protein complexes of known structure., Comment: ReVTeX4, 11 pages, 9 figures, submitted to J. Chem. Phys

In general, the direct application of the Jarzynski equality (JE) to reconstruct potentials of mean force (PMFs) from a small number of nonequilibrium unidirectional steered molecular dynamics (SMD) paths is hindered by the lack of sampling of extremely rare paths with negative dissipative work. Such trajectories, that transiently violate the second law, are crucial for the validity of JE. As a solution to this daunting problem, we propose a simple and efficient method, referred to as the FR method, for calculating simultaneously both the PMF U(z) and the corresponding diffusion coefficient D(z) along a reaction coordinate z for a classical many particle system by employing a small number of fast SMD pullings in both forward (F) and time reverse (R) directions, without invoking JE. By employing Crook's transient fluctuation theorem (that is more general than JE) and the stiff spring approximation, we show that: (i) the mean dissipative work W_d in the F and R pullings are equal, (ii) both U(z) and W_d can be expressed in terms of the easily calculable mean work of the F and R processes, and (iii) D(z) can be expressed in terms of the slope of W_d. To test its viability, the FR method is applied to determine U(z) and D(z) of single-file water molecules in single-walled carbon nanotubes (SWNTs). The obtained U(z) is found to be in very good agreement with the results from other PMF calculation methods, e.g., umbrella sampling. Finally, U(z) and D(z) are used as input in a stochastic model, based on the Fokker-Planck equation, for describing water transport through SWNTs on a mesoscopic time scale that in general is inaccessible to MD simulations., Comment: ReVTeX4, 13 pages, 6 EPS figures, Submitted to Journal of Chemical Physics

Light harvesting complexes 2 (LH2) from Rhodospirillum (Rs.) molischianum and Rhodopseudomonas (Rps.) acidophila form ring complexes out of eight or nine identical subunits, respectively. Here, we investigate computationally what factors govern the different ring sizes. Starting from the crystal structure geometries, we embed two subunits of each species into their native lipid-bilayer/water environment. Using molecular dynamics simulations with umbrella sampling and steered molecular dynamics, we probe the free energy profiles along two reaction coordinates, the angle and the distance between two subunits. We find that two subunits prefer to arrange at distinctly different angles, depending on the species, at about 42.5 deg for Rs. molischianum and at about 38.5 deg for Rps. acidophila, which is likely to be an important factor contributing to the assembly into different ring sizes. Our calculations suggest a key role of surface contacts within the transmembrane domain in constraining these angles, whereas the strongest interactions stabilizing the subunit dimers are found in the C-, and to a lesser extent, N-terminal domains. The presented computational approach provides a promising starting point to investigate the factors contributing to the assembly of protein complexes, in particular if combined with modeling of genetic variants., Comment: 28 pages, 7 figures, LaTeX2e - requires elsart.cls (included), submitted to Chemical Physics

Daily temperature anomaly records are analyzed (61 for Australia, 18 for Hungary) by means of detrended fluctuation analysis. Positive long range asymptotic correlations extending up to 5-10 years are detected for each case. Contrary to earlier claims, the correlation exponent is not universal for continental stations. Interestingly, the dominant factor is geographic latitude over Australia: the general tendency is a decrease of correlation exponent with increasing distance from the equator. This tendency is in a complete agreement with the results found by Tsonis et al. (1999) for 500-hPa height anomalies in the northern hemisphere. The variance of fluctuations exhibits an opposite trend, the larger is the distance from the equator, the larger the amplitude of intrinsic fluctuations. The presence of Tropospheric Biennial Oscillation is clearly identified for three stations at the north-eastern edge of the Australian continent., Comment: accepted for publication in Meteorology and Atmopsheric Physics

We compare the spectral properties of long meteorological temperature records with laboratory measurements in small convection cells. Surprisingly, the atmospheric boundary layer sampled on a daily scale shares the statistical properties of temperature fluctuations in small-scale experiments. This fact can be explained by the hydrodynamical similarity between these seemingly very different systems. The results suggest that the dynamics of daily temperature fluctuations is determined by the soft turbulent state of the atmospheric boundary layer in continental climate., Comment: 10 pages Latex

We measured experimentally the static friction force $F_s$ on the surface of a glass rod immersed in dry sand. We observed that $F_s$ is extremely sensitive to the closeness of packing of grains. A linear increase of the grain-density yields to an exponentially increasing friction force. We also report on a novel periodicity of $F_s$ during gradual pulling out of the rod. Our observations demonstrate the central role of grain bridges and arches in the macroscopic properties of granular packings., Comment: plain tex, 6 pages, to appear in Phys.Rev.E

In this work we compare the spectral properties of the daily medium temperature fluctuations with the experimental results of the Chicago Group, in which the local temperature fluctuations were measured in a helium cell. The results suggest that the dynamics of the daily temperature fluctuations is determined by the oft turbulent state of the atmospheric boundary layer, which state is significantly different from low dimensional chaos., Comment: 4 pages, latex, revtex, Ask for figures from vattay@nbivax.nbi.dk