相关论文: Long-Time Mean Square Displacements in Proteins
Smoothed Dissipative Particle Dynamics (SDPD) is a mesoscopic method which allows to select the level of resolution at which a fluid is simulated. In this work, we study the consistency of the resulting thermodynamic properties as a…
The Maximum Mean Discrepancy (MMD) is a widely used multivariate distance metric for two-sample testing. The standard MMD test statistic has an intractable null distribution typically requiring costly resampling or permutation approaches…
Combining elastic incoherent neutron scattering experiments at different resolutions with molecular dynamics simulations, we report the observation of a protein-like dynamical transition in linear chains of Poly(N-isopropylacrylamide). We…
Many molecules observed in the interstellar medium are thought to result from thermal desorption of ices. Parameters such as desorption energy and pre-exponential frequency factor are essential to describe the desorption of molecules.…
The formation of biomolecular condensates inside cells often involve intrinsically disordered proteins (IDPs), and several of these IDPs are also capable of forming droplet-like dense assemblies on their own, through liquid-liquid phase…
Quantifying the effects of amino acid mutations in proteins presents a significant challenge due to the vast combinations of residue sites and amino acid types, making experimental approaches costly and time-consuming. The Potts model has…
Particle density fluctuations in the scrape-off layer of magnetically confined plasmas, as measured by gas-puff imaging or Langmuir probes, are modeled as the realization of a stochastic process in which a superposition of pulses with a…
We present new 3D magnetohydrodynamic (MHD) simulations of a supernova-driven, stratified interstellar medium. These simulations were run using the Waagan (2009) positivity preserving scheme for ideal MHD implemented in the Flash code. The…
This work develops a multiscale solution decomposition (MSD) method for nonlocal-in-time problems to separate a series of known terms with multiscale singularity from the original singular solution such that the remaining unknown part…
A coarse-grained simulation method to predict NMR spectra of ions diffusing in porous carbons is proposed. The coarse-grained model uses input from molecular dynamics simulations such as the free-energy profile for ionic adsorption, and…
Mathematically modeling complex transport phenomena at the molecular level can be a powerful tool for identifying transport mechanisms and predicting macroscopic properties. We use two different stochastic time series models, parameterized…
Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…
Markov state models (MSMs) have been widely used to analyze computer simulations of various biomolecular systems. They can capture conformational transitions much slower than an average or maximal length of a single molecular dynamics (MD)…
Thermal motion in complex fluids is a complicated stochastic process but ubiquitously exhibits initial ballistic, intermediate sub-diffusive, and long-time non-Gaussian diffusive motion, unless interrupted. Despite its relevance to numerous…
Level density $\rho$ is derived for a finite system with strongly interacting nucleons at a given energy E, neutron N and proton Z particle numbers, projection of the angular momentum M, and other integrals of motion, within the…
The molecular motion in heterogeneous media displays anomalous diffusion by the mean-squared displacement $\langle X^2(t) \rangle = 2 D t^\alpha$. Motivated by experiments reporting populations of the anomalous diffusion parameters $\alpha$…
Motion in bounded domains is a fundamental concept in various fields, including billiard dynamics and random walks on finite lattices, with important applications in physics, ecology and biology. An important universal property related to…
In one-dimensional (1D) quantum gases, the momentum distribution (MD) of the atoms is a standard experimental observable, routinely measured in various experimental setups. The MD is sensitive to correlations, and it is notoriously hard to…
Supersonic turbulence in the interstellar medium (ISM) is believed to decay rapidly within a flow crossing time irrespective of the degree of magnetization. However, this general consensus of decaying magnetohydrodynamic (MHD) turbulence…
Small integration time steps limit molecular dynamics (MD) simulations to millisecond time scales. Markov state models (MSMs) and equation-free approaches learn low-dimensional kinetic models from MD simulation data by performing…