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Strongly interacting fermions define the properties of complex matter at all densities, from atomic nuclei to modern solid state materials and neutron stars. Ultracold atomic Fermi gases have emerged as a pristine platform for the study of…
Binding energy is a fundamental thermodynamic property that governs molecular interactions, playing a crucial role in fields such as healthcare and the natural sciences. It is particularly relevant in drug development, vaccine design, and…
We present a machine learning framework for modeling protein dynamics. Our approach uses L1-regularized, reversible hidden Markov models to understand large protein datasets generated via molecular dynamics simulations. Our model is…
Aquaporins (AQPs) are a family of transmembrane channels that are found from archaea, eubacteria, and fungi kingdoms to plants and animals. These proteins play a major role in water and small solutes transport across biological cell…
We study a large data set of protein structure ensembles of very diverse sizes determined by nuclear magnetic resonance. By examining the distance-dependent correlations in the displacement of residues pairs and conducting finite size…
Giant unilamellar vesicles (GUVs) composed of as few as three lipid species can phase separate into small-scale lipid domains with stripes and dots patterns. These patterns have been experimentally characterized in terms of how their size…
Cytoskeletons are self-organized networks based on polymerized proteins: actin, tubulin, and driven by motor proteins, such as myosin, kinesin and dynein. Their positive Darwinian evolution enables them to approach optimized functionality…
Lipid bilayers forming biological membranes are known to behave as viscous 2D fluids on submicrometer scales; usually they contain a large number of active protein inclusions. Recently, it has been shown [Proc. Nat. Acad. Sci. USA 112,…
Metamorphic proteins like Lymphotactin are a notable exception of the empirical principle that structured natural proteins possess a unique three dimensional structure. In particular, the human chemokine lymphotactin protein (Ltn) exists in…
Discovering disease pathways, which can be defined as sets of proteins associated with a given disease, is an important problem that has the potential to provide clinically actionable insights for disease diagnosis, prognosis, and…
Of the twenty amino acids used in proteins, ten were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth…
Phase-separated biomolecular condensates containing proteins and RNAs can assemble into higher-order structures by forming thermodynamically stable interfaces between immiscible phases. Using a minimal model of a protein/RNA interaction…
The thesis examines in detail the folding and unfolding processes of a number of proteins including hbSBD, DDLNF4, single and multi Ubiquitin. Using simplified coarse-grained off-lattice Go model and CD experiments we have shown the…
Cellular membranes exhibit a large variety of shapes, strongly coupled to their function. Many biological processes involve dynamic reshaping of membranes, usually mediated by proteins. This interaction works both ways: while proteins…
Antimicrobial peptides (AMPs) are anti-infectives that have potential as a novel and untapped class of biotherapeutics. Modes of action of antimicrobial peptides imply interaction with cell envelope. Comprehensive understanding of…
Various biological sensory systems exhibit a response to a relative change of the stimulus, often referred to as fold-change detection. In the last few years fold-change detecting mechanisms, based on transcriptional networks, have been…
Despite the recognized importance of the multi-scale spatio-temporal organization of proteins, most computational tools can only access a limited spectrum of time and spatial scales, thereby ignoring the effects on protein behavior of the…
The nodal surfaces of the many-body wavefunction are fundamental geometric features that encode critical information regarding particle statistics and their interaction. Directly probing these structures, particularly in correlated quantum…
Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of…
It is pointed out that the mystery of how biological systems measure their lengths vanishes away if one premises that they have discovered a way to generate linear waves analogous to compressional sound. These can be used to detect length…