Related papers: Harnessing the Peripheral Surface Information Entr…
Background:Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error…
The two-phase thermodynamic (2PT) model {[}J. Chem. Phys., \textbf{119}, 11792 (2003){]} provides a promising paradigm to efficiently determine the ionic entropies of liquids from molecular dynamics (MD). In this model, the vibrational…
We present a numerical study of the statistical properties of the potential energy landscape of a simple model for strong network-forming liquids. The model is a system of spherical particles interacting through a square well potential,…
Because protein-protein interactions (PPIs) are crucial to understand living systems, harvesting these data is essential to probe disease development and discern gene/protein functions and biological processes. Some curated datasets contain…
Reconfigurable intelligent surface (RIS)-aided wireless communications have drawn significant attention recently. We study the physical layer security of the downlink RIS-aided transmission framework for randomly located users in the…
Protein-surface interactions are ubiquitous in biological processes and bioengineering, yet are not fully understood. In biosensors, a key factor determining the sensitivity and thus the performance of the device is the orientation of the…
As a common view the hydrophobic association between molecular-scale binding partners is supposed to be dominantly driven by entropy. Recent calorimetric experiments and computer simulations heavily challenge this established paradigm by…
An information theory model is used to construct a molecular explanation why hydrophobic solvation entropies measured in calorimetry of protein unfolding converge at a common temperature. The entropy convergence follows from the weak…
A self-consistent expression for the surface recombination velocity $S$ and the surface Fermi level unpinning energy as a function of light excitation power ($P$) is presented for n- and p-type semiconductors doped above the 10$^{16}$…
In the post-Moore era, the need for efficient solutions to non-deterministic polynomial-time (NP) problems is becoming more pressing. In this context, the Ising model implemented by the probabilistic computing systems with probabilistic…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…
Antibody-antigen interactions play a crucial role in identifying and neutralizing harmful foreign molecules. In this paper, we investigate the optimal representation for predicting the binding sites in the two molecules and emphasize the…
The probability distribution of sequences with maximum entropy that satisfies a given amino acid composition at each site and a given pairwise amino acid frequency at each site pair is a Boltzmann distribution with $\exp(-\psi_N)$, where…
For substitutional alloys, typically refered to as classical discrete systems under constant composition, we theoretically examine the role of hidden structure information on evolution of nonlinearity (i.e., correspondence between a set of…
Protons at the water/vapor interface are relevant for atmospheric and environmental processes, yet to characterize their surface affinity on the quantitative level is still challenging. Here we utilize phase-sensitive sum-frequency…
Is protein secondary structure primarily determined by local interactions between residues closely spaced along the amino acid backbone, or by non-local tertiary interactions? To answer this question we have measured the entropy densities…
The calculation of thermodynamic properties of biochemical systems typically requires the use of resource-intensive molecular simulation methods. One example thereof is the thermodynamic profiling of hydration sites, i.e. high-probability…
The kinetics of intrinsic and dopant-enhanced solid phase epitaxy (SPE) are stud- ied in buried amorphous Si (a-Si) layers in which SPE is not retarded by H. As, P, B and Al profiles were formed by multiple energy ion implantation over a…
Phase transitions in one-dimensional lattice systems are well established and have been extensively studied within both Hermitian and non-Hermitian frameworks. In this work, we extend this understanding to a more general setting by…
Proteins involved in signaling pathways represent an interesting target for experimental analysis by ODNP (Overhauser Dynamic Nuclear Polarization), which determines the translational mobility at the surface of proteins. They also represent…