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The advent of milli-kelvin scanning tunneling microscopes (STM) with inbuilt magnetic fields has opened access to the study of magnetic phenomena with atomic resolution at surfaces. In the case of single atoms adsorbed on a surface, the…

We give a phenomenological analysis of the behavior of inelastic, elastic and total cross-sections of the high energy $\textit{pp}$ interaction. In particular, we argue that the universal picture of behavior of cross-sections and their…

The dynamic nature of proteins, influenced by ligand interactions, is essential for comprehending protein function and progressing drug discovery. Traditional structure-based drug design (SBDD) approaches typically target binding sites with…

Protein motifs are conserved fragments occurred frequently in protein sequences. They have significant functions, such as active site of an enzyme. Search and clustering protein sequence motifs are computational intensive. Most existing…

We investigate the dynamics of a particle moving randomly along a disordered hetero-polymer subjected to rapid conformational changes which induce superdiffusive motion in chemical coordinates. We study the antagonistic interplay between…

A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…

Molecular dynamics simulations of interacting soft disks confined in a heterogeneous quenched matrix of soft obstacles show dynamics which is fundamentally different from that of hard disks. The interactions between the disks can enhance…

Geometry optimization is an important part of both computational materials and surface science because it is the path to finding ground state atomic structures and reaction pathways. These properties are used in the estimation of…

The existence of anharmonic localization of lattice vibrations in a perfect 3-D diatomic ionic crystal is established for the rigid-ion model by molecular dynamics simulations. For a realistic set of NaI potential parameters, an intrinsic…

The Extra-Cellular-Matrix (ECM) is a complex interconnected 3D network that provides structural support for the cells and tissues and defines organ architecture key for their healthy functioning. However, the intimate mechanisms by which…

The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling…

Here we review the development of protein scaling theory, starting from backgrounds in mathematics and statistical mechanics, and leading to biomedical applications. Evolution has organized each protein family in different ways, but scaling…

Active solids, more specifically elastic lattices embedded with polar active units, exhibit collective actuation when the elasto-active feedback, generically present in such systems, exceeds some critical value. The dynamics then…

Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…

Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their…

We show that quasi localized low-frequency modes in the vibrational spectrum can be used to construct soft spots, or regions vulnerable to rearrangement, which serve as a universal tool for the identification of flow defects in solids. We…

We investigated the energy transfer from active enzymes to their surroundings in crowded environments by measuring the diffusion of passive microscopic tracers in active solutions of ficoll and glycerol. Despite observing lower rates of…

How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…

The eukaryotic Cys2His2 zinc finger proteins bind to DNA ubiquitously at highly conserved domains, responsible for gene regulation and the spatial organization of DNA. To study and understand the zinc finger DNA-protein interaction, we use…

The dynamical characterization of proteins is crucial to understand protein function. From a microscopic point of view, protein dynamics is governed by the local atomic interactions that, in turn, trigger the functional conformational…