Search

The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in generating pathways and rate constants for rare events such as protein folding and protein binding using atomistic molecular dynamics simulations. Here we present two sets of tutorials instructing users in the best practices for preparing, carrying out, and analyzing WE simulations for various applications using the WESTPA software. The first set of more basic tutorials describes a range of simulation types, from a molecular association process in explicit solvent to more complex processes such as host-guest association, peptide conformational sampling, and protein folding. The second set ecompasses six advanced tutorials instructing users in the best practices of using key new features and plugins/extensions of the WESTPA 2.0 software package, which consists of major upgrades for larger systems and/or slower processes. The advanced tutorials demonstrate the use of the following key features: (i) a generalized resampler module for the creation of binless schemes, (ii) a minimal adaptive binning scheme for more efficient surmounting of free energy barriers, (iii) streamlined handling of large simulation datasets using an HDF5 framework, (iv) two different schemes for more efficient rate-constant estimation, (v) a Python API for simplified analysis of WE simulations, and (vi) plugins/extensions for Markovian Weighted Ensemble Milestoning and WE rule-based modeling for systems biology models. Applications of the advanced tutorials include atomistic and non-spatial models, and consist of complex processes such as protein folding and the membrane permeability of a drug-like molecule. Users are expected to already have significant experience with running conventional molecular dynamics or systems biology simulations.

Tropical cyclones (TCs) can cause severe wind and rain hazards. Unusual TC tracks and their extreme precipitation forecasts have become two difficult problems faced by conventional models of primitive equations. The case study in this paper finds that the numerical computation of the climatological component in conventional models restricts the prediction of unusual TC tracks. The climatological component should be a forcing quantity, not a predictor in the numerical integration of all models. Anomaly-based variable models can overcome the bottleneck of forecast time length or the one-week forecasting barrier, which is limited to less than one week for conventional models. The challenge in extreme precipitation forecasting is how to physically get the vertical velocity. The anomalous moisture stress modulus (AMSM), as an indicator of heavy rainfall presented in this paper, considers the two conditions associated with vertical velocity and anomalous specific humidity in the lower troposphere. Vertical velocity is produced by the orthogonal collision of horizontal anomalous airflows. [ABSTRACT FROM AUTHOR]

Initialization and the spin‐up effect are critical to model performance in the four‐dimensional variational data assimilation (4DVar) system. The incremental analysis update (IAU) technique is able to combat these problems. This study introduces the IAU technique into the 4DVar framework (IAU‐4DVar) of the operational China Meteorological Administration Global Forecast System (CMA‐GFS) and evaluates the performance of the IAU‐4DVar. In this IAU‐4DVar framework, the initial increments optimally estimated are split up into equally weighted forcing terms and integrated into the tangent model and its adjoint model. Then, the optimal estimation of the analysis increment is gradually introduced into the model integration during the assimilation window. A set of two‐month assimilation and forecast experiments were established and executed in this study, and the preliminary results show that the IAU technique can reduce the spin‐up effect of the initial analysis increment from the operational 4DVar system with digital filter initialization (DFI‐4DVar) by retaining the balance in dynamics and thermodynamics. In the optimal minimization process, the IAU‐4DVar converges faster than the DFI‐4DVar with a reduction of the computational cost of up to ca 40%. In addition, the introduction of IAU‐4DVar into the CMA‐GFS model could have a positive impact on the analysis and forecast skills relative to the operational DFI‐4DVar. [ABSTRACT FROM AUTHOR]

Tropical cyclone (TC) genesis forecasting is essential for daily operational practices during the typhoon season. The updated version of the Tropical Regional Atmosphere Model for the South China Sea (CMA-TRAMS) offers forecasters reliable numerical weather prediction (NWP) products with improved configurations and fine resolution. While traditional evaluation of typhoon forecasts has focused on track and intensity, the increasing accuracy of TC genesis forecasts calls for more comprehensive evaluation methods to assess the reliability of these predictions. This study aims to evaluate the effectiveness of the CMA-TRAMS for cyclogenesis forecasts over the western North Pacific and South China Sea. Based on previous research and typhoon observation data over five years, a set of localized, objective criteria has been proposed. The analysis results indicate that the CMA-TRAMS demonstrated superiority in cyclogenesis forecasts, predicting 6 out of 22 TCs with a forecast lead time of up to 144 h. Additionally, over 80% of the total could be predicted 72 h in advance. The model also showed an average TC genesis position error of 218.3 km, comparable to the track errors of operational models according to the annual evaluation. The study also briefly investigated the forecast of Noul (2011). The forecast field of the CMA-TRAMS depicted thermal and dynamical conditions that could trigger typhoon genesis, consistent with the analysis field. The 96-hour forecast field of the CMA-TRAMS displayed a relatively organized threedimensional structure of the typhoon. These results can enhance understanding of the mechanism behind typhoon genesis, fine-tune model configurations and dynamical frameworks, and provide reliable forecasts for forecasters. [ABSTRACT FROM AUTHOR]

We present a new force field, AMBER ff15ipq-m, for simulations of protein mimetics in applications from therapeutics to biomaterials. This force field is an expansion of the AMBER ff15ipq force field that was developed for canonical proteins and enables the modeling of four classes of artificial backbone units that are commonly used alongside natural α residues in blended or "heterogeneous" backbones: chirality-reversed D-α-residues, the Cα-methylated α-residue Aib, homologated β-residues (β3) bearing proteinogenic side chains, and two cyclic β residues (βcyc; APC and ACPC). The ff15ipq-m force field includes 472 unique atomic charges and 148 unique torsion terms. Consistent with the AMBER IPolQ lineage of force fields, the charges were derived using the Implicitly Polarized Charge (IPolQ) scheme in the presence of explicit solvent. To our knowledge, no general force field reported to date models the combination of artificial building blocks examined here. In addition, we have derived Karplus coefficients for the calculation of backbone amide J-coupling constants for β3Ala and ACPC β residues. The AMBER ff15ipq-m force field reproduces experimentally observed J-coupling constants in simple tetrapeptides and maintains the expected conformational propensities in reported structures of proteins/peptides containing the artificial building blocks of interest—all on the μs timescale. These encouraging results demonstrate the power and robustness of the IPolQ lineage of force fields in modeling the structure and dynamics of natural proteins as well as mimetics with protein-inspired artificial backbones in atomic detail. [ABSTRACT FROM AUTHOR]

The persistence barrier (PB), one of the El Niño–Southern Oscillation (ENSO) properties, has exhibited a significant decadal variability, showing enhanced and weakened behavior before and after the late 1970s, respectively. In the present study, both the theoretical solution and the observations indicate that the variability of PB intensity is linearly proportional to the seasonal amplitude of ENSO growth rate, which accounts for the ENSO PB decadal variability. With further use of the Bjerknes–Jin (BJ) index analysis, we find that the decadal reduction in PB intensity since the late 1970s is mainly attributed to the mean advection and the thermocline feedback. In addition, the stronger spring thermal damping delayed the timing of PB in the 1980s and 1990s. Our study establishes a linear relationship between PB intensity and ENSO growth rate, which carries implications for understanding the ENSO predictability and the systematic changes in ENSO properties under climate change. [ABSTRACT FROM AUTHOR]

The western Pacific subtropical high (WPSH) substantially affects the climate in the Pacific and East Asia. Previous studies have revealed that the springtime Indo‐Pacific warm pool (IPWP) sea surface temperature zonal gradient (SSTG) could be used as a predictor of the subsequent summertime WPSH's intensity. Here, we find that the interannual variability of the springtime IPWP SSTG has greatly decreased after the late 1990s, accompanied by the weakened relationship between the springtime IPWP SSTG and the following summertime WPSH, which may reduce the efficiency of the springtime IPWP SSTG as a key predictor for the summertime WPSH in recent decades. This observed recent weakening IPWP SSTG–WPSH relationship could be largely contributed by the decadal shift of the El Niño–Southern Oscillation (ENSO) and the WPSH around the late 1990s. The ENSO regime shift from the eastern Pacific (EP) type to the central Pacific (CP) type could alter the spatial pattern of the springtime IPWP sea surface temperature (SST) dipole and further weaken the local air–sea interaction between the underlying IPWP SST and the WPSH. From another perspective of the WPSH decadal shift, the WPSH‐related first leading mode before (after) the late 1990s, characterized by a large‐scale uniform (dipole) pattern with an oscillating period of ~4–5 year (~2–3 year), tended to promote a stronger (weaker) linkage with the springtime IPWP SSTG. In addition, the recent enhancement of the tropical Atlantic SST influences is considered to possibly promote the decadal shifts of the ENSO and the WPSH‐related leading mode. After the springtime tropical Atlantic SST was added as a predictor, the predicting skills of the empirical equation for the summertime WPSH could be substantially improved. The results herein have important implications for the further improvement of the seasonal WPSH prediction, which is of great practical significance in the prevention and mitigation of climate disasters. [ABSTRACT FROM AUTHOR]

A record-breaking severe ozone (O3) pollution episode occurred in the Pearl River Delta (PRD) in early autumn 2019 when the PRD was under the influence of a Pacific subtropical high followed by Typhoon Mitag. In this study, we analyzed the effects of meteorological and photochemical processes on the O3 concentration in the PRD during this episode by carrying out the Weather Research Forecast–Community Multiscale Air Quality (WRF-CMAQ) model simulations. Results showed that low relative humidity, high boundary layer height, weak northerly surface wind, and strong downdrafts were the main meteorological factors contributing to O3 pollution. Moreover, delayed sea breezes that lasted into the night would transport O3 from the sea back to the land and resulted in secondary O3 maxima at night. In addition, O3 and its precursors stored in the residual layer above the surface layer at night can be mixed down to the surface in the next morning, further enhancing the daytime ground-level O3 concentration on the following day. Photochemical production of O3 , with a daytime average production rate of about 7.2 ppbh-1 (parts per billion), is found to be the predominate positive contributor to the O3 budget of the boundary layer (0–1260 m) during the entire O3 episode, while the horizontal and vertical transport fluxes are the dominant negative contributors. This O3 episode accounted for 10 out of the yearly total of 51 d when the maximum daily 8 h average (MDA8) O3 concentration exceeded the national standard of 75 ppb in the PRD in 2019. Based on these results, we propose that the enhanced photochemical production of O3 during the episode is a major cause of the most severe O3 pollution year since the official O3 observation started in the PRD in 2006. Moreover, since this O3 episode is a synoptic-scale phenomenon covering the entire eastern China, we also suggest that the enhanced photochemical production of O3 in this O3 episode is a major cause of the extraordinarily high O3 concentrations observed in eastern China in 2019. [ABSTRACT FROM AUTHOR]

Six dust storms that originated from Mongolia and moved to northern China in Spring 2021 are investigated by the anomaly variable‐based analysis method, which is compared to the traditional total‐variable based analysis method. Strong surface wind is a force to form dust storms as commonly known in current practice. However, dust area depicted by total‐wind model product analysis and operational forecast has a large bias to observation even for leading 24 hr. The analysis method of anomaly based variables showed that the domain of an airborne dust storm observed from satellite images is usually located between two neighboring convergence lines of 850 hPa anomalous winds. This connection of dust storm associated with the anomalous wind convergence extends southwestward from an anomalous cyclone and moves from Mongolia to northern China or Northeast China. It is thermodynamically associated with an anomalous thermal contrast, which has a spatial structure of wind, temperature, and geopotential height anomalies in the troposphere. We further found that numerical weather prediction products of the ECMWF model are able to indicate the anomalous wind pattern with lead times of 4–8 days by applying the anomaly based analysis approach. Therefore, this approach can not only depict dust area better but also reveal predictors much easier compared to the traditional total‐variable or full‐field‐based analysis method. Key Points: Dust storm can be well detected by the anomaly based analysis of atmospheric variablesA dust domain is located between two neighboring convergence lines of 850 hPa anomalous windsThe ECMWF model can predict the anomalous wind pattern for leading 4–8 days [ABSTRACT FROM AUTHOR]

Previous studies showed that 4D-Var technique used for data assimilation could be modified for weather control. This study demonstrates the ability of 4D-Var to influence the future path of a tropical cyclone by calculating perturbations in WRF simulation. Given the background error covariance matrix, the initial field is improved by the vortex dynamic initialization technique. Our results show that 4D-Var can be applied to control the trajectory of simulated tropical cyclones by producing "optimal" perturbations. In the numerical simulation experiment of Typhoon Mitag in 2019, after this kind of weather control similar to data assimilation, the tropical cyclone moved obviously, and the damaging wind over the coastline weakened. The prediction results after the initial field modified by 4D-Var have a great change, and the position of the tropical cyclone moved about 0.5° southeastward after assimilation, which misses the southeast coast of China. Moreover, the damaging wind is also weakened. Since the 4D-Var is premised on the assumption that the model is perfect and does not consider the model error, then the research plan to consider model error and introduce new methods is discussed in the paper. [ABSTRACT FROM AUTHOR]

It is well‐known that the increasing zonal‐mean trend of sea‐ice concentration (SIC) surrounding Antarctica is up to 2015 so this paper first summarized this trend with opposing regional trends in each season along the latitude band 60°–70°S during 1979–2015. The surface wind trends can partly explain the observed regional SIC trends. By analysing the surface wind, as well as the tropospheric geopotential height (GPH) and temperature trends, the study revealed that the increasing zonal‐mean SIC trend and opposing regional SIC trends surrounding Antarctica are vertically associated with GPH and temperature trends in the troposphere. This relationship is also found in extreme years for seven SIC maximum and four SIC minimum autumns from 1979 to 2015, particularly reconfirmed in the two SIC minimum autumns of 2017 and 2018, indicating that a positive regional SIC anomaly is vertically associated with an anomalously cold air mass centred around 850 hPa in the troposphere which is located beneath a negative GPH anomaly at the upper troposphere, and vice versa. [ABSTRACT FROM AUTHOR]

To mark the 10th anniversary of the Melbourne Journal of International Law, we were inspired to reflect upon the past and to consider our future; to recall the scholarly contributions [...]

The Arctic cell as a reversed and closed loop next to the Polar cell has been recently revealed in the Northern Hemisphere (NH). In this paper, we study the interannual variability of the Arctic and Polar cell strengths during 1979-2012, and their influence on surface air temperature (SAT), precipitation, and sea-ice concentration (SIC) at mid- and high-latitudes of the NH. We show that there is a significant negative correlation between the Arctic and Polar cell strengths. Both the Arctic and Polar cell strengths can well indicate the recurring climatic anomalies of SAT, precipitation, and SIC in their extreme winters. The surface large-scale cold-warm and dry-wet anomalous patterns in these extreme winters are directly linked with the vertical structure of height and temperature anomalies in the troposphere. Results suggest that the past climatic anomalies are better indicated by the strength anomalies of the Polar and Arctic cells than the traditional indices of mid-high latitude pattern such as the Arctic Oscillation and North Atlantic Oscillation. This study illustrates a three-dimensional picture of atmospheric variable anomalies in the troposphere that result in surface climatic anomalies. [ABSTRACT FROM AUTHOR]

ABSTRACT In the summer of 2010, western Russia experienced extreme heat, which was noted for its exceptional spatial spread, long duration, high intensity and impacts. We use an anomaly-based approach to decompose atmospheric variables into daily climatic components and anomalies from two reanalysis datasets. We show that a surface heat wave event results from a downward extension of an anomalously warm air column below a centre of positive geopotential height anomalies in the upper troposphere. Therefore, we use this approach to analyse all summer regional heat wave events with spatial scales larger than 2000 km and durations greater than 5 days over western Eurasia from 1980 to 2014. Our results demonstrate that the rapid increase in regional heat wave events over western Eurasia since 2010 is a direct response to the increasing frequency of large-scale, quasi-stationary positive centres of maximum height anomalies in the upper troposphere. [ABSTRACT FROM AUTHOR]

The global monsoon domain has been recently determined utilizing two criteria: difference of local maximum and minimum pentad-mean precipitation rates exceeding 4 mm day, and wind reversal of low-level cross-equatorial flow. In this paper, 22 major dry-wet alteration regions under six categories were first derived through the k-means clustering method from the climatological evolution of global precipitation. Considering the seasonal influences of the low-level cross-equatorial flow in these major dry-wet alternation regions, the global monsoon was objectively divided into 16 major regions under five climatological precipitation categories. Nine monsoon regions are distributed between Asia and Australia while four regions are from Africa to the Southwest Indian Ocean and three regions in Americas. Precipitation trends during rainy seasons of 1981-2010 were examined in the 16 monsoon regions. Four regions with decreasing trends of precipitation are located in Africa and the Southwest Indian Ocean while three regions with increasing trends are situated in Americas. Six regions of increasing precipitation trends are concentrated in Asia and the biggest increasing trend is found in south China. [ABSTRACT FROM AUTHOR]

In this study, the seasonal variations of Madden-Julian Oscillation (MJO) are simulated with a 2.5-layer model governed by a set of perturbation equations, considering the effects of boundary layer friction convergence, diabatic heating, moisture feedback and background flow, under a non-resting basic state. The governing perturbation equations are written under a basic state defined by the 30-year climatology of observation (reanalysis), in which daily/monthly climatic wind, geopotential and moisture act as a background forcing influencing the evolution and propagation of MJO. Under this climatic background state, the precipitation of basic state is no longer zero but equal to the 30-year precipitation climatology, which is generally larger in the tropical region and has a dominant seasonal cycle in the subtropical region. Diabatic heating of convection is the key factor that produces the coupled Rossby-Kelvin structure of MJO and is a function of precipitation perturbation in the model. In common practice, precipitation perturbation can be derived from precipitation parametrization schemes, which usually consider only positive values during calculation because negative precipitation does not physically exist in the real world. However, the model in the study is run under a non-zero rainfall background, thus precipitation perturbation is not constraint to be non-negative. In this case, "negative precipitation" area is referred to as abnormally dry area, and leads to "diabatic cooling" (i.e. weaker diabatic heating compared to the basic state) to the troposphere.Model simulations show that the climatic state and "negative precipitation" are two indispensable factors to the MJO seasonal variations. The climatic state provides a crucial background circulation and moisture distribution that favors MJOs / Boreal Summer Intraseasonal Oscillations (BSISOs), as reported in previous studies. On top of the climatic state, our results indicate that the "negative precipitation" effect is also essential to the simulation of MJO in different seasons. The MJO seasonal variations are less obvious if the model only incorporates positive precipitation. Results also reveal that the "negative precipitation" effectively damps shortwaves. [ABSTRACT FROM AUTHOR]

Sequence-encoded protein folding is a ubiquitous biological process that has been successfully engineered in a range of oligomeric molecules with artificial backbone chemical connectivity. A remarkable aspect of protein folding is the contrast between the rapid rates at which most sequences in nature fold and the vast number of conformational states possible in an unfolded chain with hundreds of rotatable bonds. Research efforts spanning several decades have sought to elucidate the fundamental chemical principles that dictate the speed and mechanism of natural protein folding. In contrast, little is known about how protein mimetic entities transition between an unfolded and folded state. Here, we report effects of altered backbone connectivity on the folding kinetics and mechanism of the B domain of Staphylococcal protein A (BdpA), an ultrafast-folding sequence. A combination of experimental biophysical analysis and atomistic molecular dynamics simulations performed on the prototype protein and several heterogeneous-backbone variants reveal the interplay among backbone flexibility, folding rates, and structural details of the transition state ensemble. Collectively, these findings suggest a significant degree of plasticity in the mechanisms that can give rise to ultrafast folding in the BdpA sequence and provide atomic level insights into how protein mimetic chains adopt an ordered folded state., Competing Interests: L. T. C. is a member of the Scientific Advisory Board of OpenEye Scientific, Cadence Molecular Sciences; and an Open Science Fellow with Psivant Therapeutics., (This journal is © The Royal Society of Chemistry.)

The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in generating pathways and rate constants for rare events such as protein folding and protein binding using atomistic molecular dynamics simulations. Here we present two sets of tutorials instructing users in the best practices for preparing, carrying out, and analyzing WE simulations for various applications using the WESTPA software. The first set of more basic tutorials describes a range of simulation types, from a molecular association process in explicit solvent to more complex processes such as host-guest association, peptide conformational sampling, and protein folding. The second set ecompasses six advanced tutorials instructing users in the best practices of using key new features and plugins/extensions of the WESTPA 2.0 software package, which consists of major upgrades for larger systems and/or slower processes. The advanced tutorials demonstrate the use of the following key features: (i) a generalized resampler module for the creation of "binless" schemes, (ii) a minimal adaptive binning scheme for more efficient surmounting of free energy barriers, (iii) streamlined handling of large simulation datasets using an HDF5 framework, (iv) two different schemes for more efficient rate-constant estimation, (v) a Python API for simplified analysis of WE simulations, and (vi) plugins/extensions for Markovian Weighted Ensemble Milestoning and WE rule-based modeling for systems biology models. Applications of the advanced tutorials include atomistic and non-spatial models, and consist of complex processes such as protein folding and the membrane permeability of a drug-like molecule. Users are expected to already have significant experience with running conventional molecular dynamics or systems biology simulations., Competing Interests: 10Potentially Conflicting Interests The authors declare the following competing financial interests): L.T.C. is a current member of the Scientific Advisory Board of OpenEye Scientific and an Open Science Fellow with Psivant Sciences. S Zhang, JP Thompson, and DN LeBard are employees of OpenEye Scientific.