相关论文: Unbiased simulation of structural transitions in c…
The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide…
We introduce an efficient and robust method to compute alchemical free energy differences, resulting from the application of multiple walker Adaptive Biasing Force (ABF) in conjunction with strongly damped Langevin $\lambda$-dynamics.…
We employ the Partially Saturated Cells Method (PSM) to model the interaction between the fluid flow and solid moving objects as an extension to the conventional lattice Boltzmann method. We introduce an efficient and accurate method for…
Continuum Monte-Carlo simulations at constant pressure are performed on short chain molecules at surfaces. The rodlike chains, consisting of seven effective monomers, are attached at one end to a flat twodimensional substrate. It is found…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
Neural network-based molecular dynamics (NNMD) simulations incorporating long-range electrostatic interactions have significantly extended the applicability to heterogeneous and ionic systems, enabling effective modeling critical physical…
Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…
Finite element analysis of solid mechanics is a foundational tool of modern engineering, with low-order finite element methods and assembled sparse matrices representing the industry standard for implicit analysis. We use performance models…
Structurally disordered materials continue to pose fundamental questions, including that of how different disordered phases ("polyamorphs") can coexist and transform from one to another. As a widely studied case, amorphous silicon (a-Si)…
Atomistic modelling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an…
Simulating stiff materials in applications where deformations are either not significant or can safely be ignored is a pivotal task across fields. Rigid body modeling has thus long remained a fundamental tool and is, by far, the most…
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 present an information-based total-energy optimization method to produce nearly defect-free structural models of amorphous silicon. Using geometrical, structural and topological information from disordered tetrahedral networks, we have…
We compare two recently proposed methods for the characterization of phase transitions in small systems. The usefulness of these techniques is evaluated for the case of structural transition in alanine-based peptides.
High-dimensional recordings of dynamical processes are often characterized by a much smaller set of effective variables, evolving on low-dimensional manifolds. Identifying these latent dynamics requires solving two intertwined problems:…
By considering momentum transfer in the Fermi constraint procedure, the stability of the initial nuclei and fragments produced in heavy-ion collisions can be further improved in the quantum molecular dynamics simulations. The case of the…
Engineering alloys generally exhibit multi-phase microstructures. For simulating their microstructure evolution during solid-state phase transformation, CALPHAD-guided multi-phase-field models coupled with micro-mechanics have proven to be…
Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the…
We present a loosely coupled scheme for the numerical simulation of the cardiac electro-fluid-structure interaction problem, whose solution is typically computationally intensive due to the need to suitably treat the coupling of the…
In this paper, we present an efficient algorithm for the long time behavior of plasma simulations. We will focus on 4D drift-kinetic model, where the plasma's motion occurs in the plane perpendicular to the magnetic field and can be…