相关论文: Intrinsic Mean Square Displacements in Proteins
High-density polyethylene (HDPE) is used in applications ranging from cooling water pipelines in nuclear power plants and distribution pipelines for natural gas and hydrogen to biomedical implants. Embedded crack-like flaws form within HDPE…
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 $\alpha$…
Studies of liquid water in its supercooled region have led to many insights into the structure and behavior of water. While bulk water freezes at its homogeneous nucleation temperature of approximately 235 K, for protein hydration water,…
Machine learning techniques are used to explore the intrinsic origins of the hydrodynamic thermal transport and to find new materials interesting for science and engineering. The hydrodynamic thermal transport is governed intrinsically by…
An ab initio equation of motion method is introduced to calculate the temperature-dependent mean square vibrational amplitudes which appear in the Debye-Waller factors in x-ray absorption, x-ray scattering, and related spectra. The approach…
The mechanisms of cold- and pressure-denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here we study several cases of proteins, with or without a unique native state, with or…
Differential Mobility Spectrometry (DMS), also known as Field Asymmetric Ion Mobility Spectrometry, is a rapid and affordable technology for extracting information from gas phase samples containing complex volatile organic compounds, and…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
We present a model of the dynamical transition of atomic displacements in proteins. Increased mean-square displacement at higher temperatures is caused by softening of the vibrational force constant by electrostatic and van der Waals forces…
Adsorption processes play a fundamental role in molecular transport through nanofluidic systems, but their signatures in measured signals are often hard to distinguish from other processes like diffusion. In this paper, we derive an…
For a given metric measure space $(X,d,\mu)$ we consider finite samples of points, calculate the matrix of distances between them and then reconstruct the points in some finite-dimensional space using the multidimensional scaling (MDS)…
We construct a Wasserstein gradient flow of the maximum mean discrepancy (MMD) and study its convergence properties. The MMD is an integral probability metric defined for a reproducing kernel Hilbert space (RKHS), and serves as a metric on…
Scattering experiments can be leveraged to extract the effective properties of a heterogeneous metamaterial slab based on multi-point measurements in surrounding media. In this technique, two measurements are made in the ambient media on…
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.…
Myoglobin (Mb) binds diatomic ligands, like O$_2$, CO, and NO, in a cavity that is only transiently accessible. Crystallography and molecular simulations show that the ligands can migrate through an extensive network of transiently…
A parametric oscillator with damping driven by white noise is studied. The mean square displacement (MSD) in the long-time limit is derived analytically for the case that the static force vanishes, which was not treated in the past work…
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…
Anomalous diffusion occurs in many physical and biological phenomena, when the growth of the mean squared displacement (MSD) with time has an exponent different from one. We show that recurrent neural networks (RNN) can efficiently…
We consider the problem of subspace estimation in a Bayesian setting. Since we are operating in the Grassmann manifold, the usual approach which consists of minimizing the mean square error (MSE) between the true subspace $U$ and its…
The optimum design of high-sensitivity Superconducting Quantum Interference Devices (SQUIDs) and other devices based on thin HTS films requires accurate inductance modeling. This needs the London penetration depth $\lambda$ to be well…