相关论文: Unbiased simulation of structural transitions in c…
Controlling polymorphism in molecular crystals is crucial in the pharmaceutical, dye, and pesticide industries. However, its theoretical description is extremely challenging, due to the associated long timescales ($ > 1 \, \mu s$). We…
Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid domains linked by generalized (rotational and stretching) harmonic springs. We present a method to obtain the elastic parameters and overdamped…
Glycans are structurally diverse and flexible biomolecules that play key roles in many biological processes. Their conformational variability makes the modeling of their interactions with proteins particularly challenging. This chapter…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
We present GridFF, an efficient method for simulating molecules on rigid substrates, derived from techniques used in protein-ligand docking in biochemistry. By projecting molecule-substrate interactions onto precomputed spatial grids with…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
We examine the structural and dynamic properties of confined binary hard-sphere mixtures designed to mimic realizable colloidal thin films. Using computer simulations, governed by either Newtonian or overdamped Langevin dynamics, together…
We introduce a general-purpose framework for interconnecting scientific simulation programs using a homogeneous, unified interface. Our framework is intrinsically parallel, and conveniently separates all component numerical modules in…
Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding process and prediction of the native fold of proteins are two major unsolved problems in biophysics. Here, we show successful all-atom ab initio…
We propose a method for inference on moderately high-dimensional, nonlinear, non-Gaussian, partially observed Markov process models for which the transition density is not analytically tractable. Markov processes with intractable transition…
Developing efficient path integral (PI) methods for atomistic simulations of vibrational spectra in heterogeneous condensed phases and interfaces has long been a challenging task. Here, we present the h-CMD method, short for hybrid centroid…
We present a general framework for obtaining robust bounds on the nature of dark matter using cosmological $N$-body simulations and Lyman-alpha forest data. We construct an emulator of hydrodynamical simulations, which is a flexible,…
In this paper we present the results of a large-scale numerical investigation of structural properties of a model of cell membrane, simulated as a bilayer of flexible molecules in vacuum. The study was performed by carrying out extensive…
The dynamic emulation of non-linear deterministic computer codes where the output is a time series, possibly multivariate, is examined. Such computer models simulate the evolution of some real-world phenomenon over time, for example models…
Quantum simulations of many-body systems offer novel methods for probing the dynamics of the Standard Model and its constituent gauge theories. Extracting low-energy predictions from such simulations rely on formulating…
Here we describe an approach for simulating electronic structure on quantum computers with significantly lower asymptotic complexity than prior work. The approach uses a real-space first-quantised representation of the molecular Hamiltonian…
Quantum simulation enables study of many-body systems in non-equilibrium by mapping to a controllable quantum system, providing a new tool for computational intractable problems. Here, using a programmable quantum processor with a chain of…
By means of molecular-dynamics simulations, temperature driven diffusionless structural phase transitions in equi- and nearly equiatomic ordered nickel-titanium alloys were investigated. For this purpose, a model potential from the…
The nonlinearity of dynamics in systems biology makes it hard to infer them from experimental data. Simple linear models are computationally efficient, but cannot incorporate these important nonlinearities. An adaptive method based on the…
Non-covalent interactions are a key ingredient to determine the structure, stability, and dynamics of materials, molecules, and biological complexes. However, accurately capturing these interactions is a complex quantum many-body problem,…