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The stabilization of macromolecules is fundamental to developing biological formulations, such as vaccines and protein therapeutics. In this study, we employ coarse grained polymer models to investigate the impact of four sugars:…
Biomolecular condensates play essential roles in cellular processes, and recent efforts have focused on understanding their assembly and rational design principles. In this study, we have employed an explicit-solvent minimal statistical…
We have studied the structure and properties of potassium clusters containing even number of atoms ranging from 2 to 20 at the ab initio level. The geometry optimization calculations are performed using all-electron density functional…
Current theories of heteropolymers are inherently macrpscopic, but are applied to folding proteins which are only mesoscopic. In these theories, one computes the averaged free energy over sequences, always assuming that it is self-averaging…
Monoclonal antibody solutions are set to become a major therapeutic tool in the years to come, capable of targeting various diseases by clever designing their antigen binding site. However, the formulation of stable solutions suitable for…
In this paper, we study the formation of clusters for stochastic interacting particle systems (SIPS) that interact through short-range attractive potentials in a periodic domain. We consider kinetic (underdamped) Langevin dynamics and focus…
We present results from a study of the X-ray cluster population that forms within the CLEF cosmological hydrodynamics simulation, a large N-body/SPH simulation of the Lambda CDM cosmology with radiative cooling, star formation and feedback.…
We introduce a set of four new publicly available N-body simulations, the most recent additions to the Texas P^3M Database. Our models probe the less studied parameter space region of moderate volume (100/h Mpc box) combined with fine mass…
We propose a polymer model for the dynamics of chromatin replication in three dimensional space. Our simulations indicate that both immobile and tracking replisomes may self-assemble during the process, reconciling previous apparently…
Using a new semi empirical method for calculating molecular polarizabilities and the Clausius Mossotti relation, we calculated the static dielectric constants of dry proteins for all structures in the protein data bank (PDB). The mean…
We investigate the structure of colloid-polymer mixtures by calculating the structure factors for the Asakura-Oosawa model in the PY approximation. We discuss the role of potential range, polymer concentration and polymer-polymer…
The structure of random sphere packings in mechanical equilibrium in prescribed stress states, as studied by molecular dynamics simulations, strongly depends on the assembling procedure. Frictionless packings in the limit of low pressure…
We demonstrate the accuracy of the hypernetted chain closure and of the mean-field approximation for the calculation of the fluid-state properties of systems interacting by means of bounded and positive-definite pair potentials with…
Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…
We present force-clamp data on the collapse of ubiquitin polyproteins in response to a quench in the force. These nonequilibrium trajectories are analyzed using a general method based on a diffusive assumption of the end-to-end length to…
While a monomer of the ubiquitous hormone insulin is the biologically active form in the human body, its hexameric assembly acts as an efficient storage unit. However, the role of water molecules in the structure, stability and dynamics of…
Enzyme-catalysed reactions involve two distinct timescales. There is a short timescale on which enzymes bind to substrate molecules to produce bound complexes, and a comparatively long timescale on which the complex is transformed into a…
In the free energy of hydration of a solute, the chemical contribution is given by the free energy required to expel water molecules from the coordination sphere and the packing contribution is given by the free energy required to create…
Here we report experiments on particle cluster settling at high Reynolds number in quiescent fluid contained in a vessel. The particles were observed to settle in a near-circular shape irrespective of the shape of the vessel cross-section…
AIMS. While weak lensing cannot resolve cluster cores and strong lensing is almost insensitive to density profiles outside the scale radius, combinations of both effects promise to constrain density profiles of galaxy clusters well, and…