Related papers: Understanding Protein-Complex Assembly through Gra…
Many complex systems in nature and society can be described in terms of networks capturing the intricate web of connections among the units they are made of. A key question is how to interpret the global organization of such networks as the…
A new method for sequence optimization in protein models is presented. The approach, which has inherited its basic philosophy from recent work by Deutsch and Kurosky [Phys. Rev. Lett. 76, 323 (1996)] by maximizing conditional probabilities…
The macroscopic behavior of the solution of a coupled system of partial differential equations arising in the modeling of reaction-diffusion processes in periodic porous media is analyzed. Our mathematical model can be used for studying…
Protein aggregation is of particular interest due to its connection with many diseases and disorders. Many factors can alter the dynamics and result of this process, one of them being the diffusivity of the monomers and aggregates in the…
Clustering aims to divide a set of points into groups. The current paradigm assumes that the grouping is well-defined (unique) given the probability model from which the data is drawn. Yet, recent experiments have uncovered several…
We present a theory to predict the structure and thermodynamics of mixtures of colloids of different diameters, building on our earlier work [J. Chem. Phys. 145, 074904 (2016)] that considered mixtures with all particles constrained to have…
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
The ability to control the crystallization behaviour (including its absence) of particles, be they biomolecules such as globular proteins, inorganic colloids, nanoparticles, or metal atoms in an alloy, is of both fundamental and…
Many proteins carry out their biological functions by forming the characteristic tertiary structures. Therefore, the search of the stable states of proteins by molecular simulations is important to understand their functions and…
This study explores the role of information entropy in understanding nuclear density distributions, including both stable configurations and non-traditional structures such as neutron halos and $\alpha$-clustering. By quantifying the…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
A general method is presented for modeling high entropy alloys as ensembles of randomly sampled, ordered configurations on a given lattice. Statistical mechanics is applied post hoc to derive the ensemble properties as a function of…
The detailed analysis of molecular structures and properties holds great potential for drug development discovery through machine learning. Developing an emergent property in the model to understand molecules would broaden the horizons for…
{\alpha}-synuclein ({\alpha}-syn) is an intrinsically disordered protein which is considered to be one of the causes of Parkinson's disease. This protein forms amyloid fibrils when in a highly concentrated solution. The fibril formation of…
The spatial organization of cell membrane glycoproteins and glycolipids is critical for mediating the binding of ligands, receptors, and macromolecules on the plasma membrane. However, we currently do not have the methods to quantify the…
In the cell, protein complexes form relying on specific interactions between their monomers. Excluded volume effects due to molecular crowding would lead to correlations between molecules even without specific interactions. What is the…
The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify…
Proteins exist as a dynamic ensemble of multiple conformations, and these motions are often crucial for their functions. However, current structure prediction methods predominantly yield a single conformation, overlooking the conformational…
Advances in experimental techniques and in theoretical models have improved our understanding of protein crystallization. But they have also left open questions regarding the protein phase behavior and self-assembly kinetics, such as why…
Motivation: Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy, and…