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Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…

Solar-driven water electrolysis requires high-performance photoelectrodes that exhibit excellent photoabsorption, superior charge transport, and optimized thermal management. In this work, we conducted a first-principles investigation to…

Shock electrodialysis (shock ED), an emerging electrokinetic process for water purification, leverages the new physics of deionization shock waves in porous media. In previous work, a simple leaky membrane model with surface conduction can…

The extension of piezoresistance coefficient extraction method was proposed, for protection from errors in estimation of the thickness of the test structure membrane. This new approach requires finding models of elements of matrix of…

The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…

Learning meaningful protein representation is important for a variety of biological downstream tasks such as structure-based drug design. Having witnessed the success of protein sequence pretraining, pretraining for structural data which is…

Elucidation of possible pathways between folded (native) and unfolded states of a protein is a challenging task, as the intermediates are often hard to detect. Here we alter the solvent environment in a controlled manner by choosing two…

Analysis has been made on a possibility of phase separation and critical point as a solution of fine particles in plasmas, extending the previous work which pointed out this as one of two such possibilities. Fine particles are treated as a…

This review article discusses some common enhanced sampling methods in relation to the process of self-assembly of biomolecules. An introduction to self-assembly and its challenges is covered followed by a brief overview of the methods and…

This chapter illustrates the use of defect physics as a conceptual and theoretical framework for understanding and designing battery materials. It starts with a methodology for first-principles studies of defects in complex transition-metal…

Porous materials are ubiquitous in various engineering and geological applications, where their permeability plays a critical role in viscous fluid flow and transport phenomena. Understanding and characterizing the microscale properties,…

Determining the spectral density of a molecular system immersed in a proteomic scaffold and in contact to a solvent is a fundamental challenge in the coarse-grained description of, e.g., electron and energy transfer dynamics. Once the…

Disordered proteins play essential roles in myriad cellular processes, yet their structural characterization remains a major challenge due to their dynamic and heterogeneous nature. We here present a community-driven initiative to address…

This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free…

Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…

This paper investigates the problem of electrophoretic motion of a polyelectrolyte capsule with a porous arbitrary charged conducting shell in an electrolyte under the action of an external electric field. The corresponding boundary value…

This chapter is devoted to the analysis of jamming and percolation behavior of two-dimensional systems of elongated particles. We consider both continuous and discrete spaces (with the special attention to the square lattice), as well the…

Two-dimensional electrophoresis has nurtured the birth of proteomics. It is however no longer the exclusive setup used in proteomics, with the development of shotgun proteomics techniques that appear more fancy and fashionable…

This paper focuses on the homogenization of high-contrast dielectric elastomer composites, materials that deform in response to electrical stimulation. The considered heterogeneous material consisting of an ambient material with inserted…

We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…