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The function of biomolecules such as proteins depends on their ability to interconvert between a wide range of structures or "conformations." Researchers have endeavored for decades to develop computational methods to predict the…
We performed two-dimensional simulated tempering (ST) simulations of the two-dimensional Ising model with different lattice sizes in order to investigate the two-dimensional ST's applicability to dealing with phase transitions and to study…
The cytoskeleton, consisting of biopolymer filaments, molecular motors, and passive crosslinking proteins, provides the internal structure of cells that facilitate movement, growth, and cell division. Understanding the microscopic…
Capturing and predicting the effective mechanical properties of highly porous cellular media still represents a significant challenge for the research community, due to their complex structural interdependencies and known size effects.…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
Protein function does not solely depend on structure but often relies on dynamical transitions between distinct conformations. Despite this fact, our ability to characterize or predict protein dynamics is substantially less developed…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
The protein dynamics are common and important for their biological functions and properties, the study of which usually involves time-consuming molecular dynamics (MD) simulations in silico. Recently, generative models has been leveraged as…
We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force (PMF) obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in…
Simulated tempering is popular method of allowing MCMC algorithms to move between modes of a multimodal target density {\pi}. One problem with simulated tempering for multimodal targets is that the weights of the various modes change for…
We present a maximum-caliber method for inferring transition rates of a Markov State Model (MSM) with perturbed equilibrium populations, given estimates of state populations and rates for an unperturbed MSM. It is similar in spirit to…
The simulated tempering (ST) is an important method to deal with systems whose phase spaces are hard to sample ergodically. However, it uses accepting probabilities weights which often demand involving and time consuming calculations. Here…
The mechanical behavior of closed-cell foams in compression is analyzed by means of the finite element simulation of a representative volume element of the microstructure. The digital model of the foam includes the most relevant details of…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
We present an efficient method to mix well converged ab initio forces with simpler and faster ones in molecular dynamics. While the cheap forces are evaluated every time step, the converged ones correct the trajectory only every n time…
A number of problems arise when long-range forces, such as those governed by Bessel functions, are used in particle-particle simulations. If a simple cut-off for the interaction is used, the system may find an equilibrium configuration at…
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…
The weighted ensemble (WE) simulation strategy provides unbiased sampling of non-equilibrium processes, such as molecular folding or binding, but the extraction of rate constants relies on characterizing steady state behavior.…
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered…
Simulated tempering (ST) is an established Markov chain Monte Carlo (MCMC) method for sampling from a multimodal density $\pi(\theta)$. Typically, ST involves introducing an auxiliary variable $k$ taking values in a finite subset of $[0,1]$…