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Electrical forces are the background of all the interactions occurring in biochemical systems. From here and by using a combination of ab-initio and ad-hoc models, we introduce the first description of electric field profiles with intrabond…
Mechanistic interpretability of biological foundation models has relied on selective feature sampling, pairwise interaction testing, and observational trajectory analysis. Each of these can introduce systematic bias. Here we present three…
Physical interactions between proteins are often difficult to decipher. The aim of this paper is to present an algorithm designed to recognize binding patches and supporting structural scaffolds of interacting heterodimer protein chains…
The macromolecules that encode and translate information in living systems, DNA and RNA, exhibit distinctive structural asymmetries, including homochirality or mirror image asymmetry and $3' - 5'$ directionality, that are invariant across…
Timely up- or down-regulation of gene expression is crucial for cellular differentiation and function. While gene upregulation via transcriptional activators has been extensively investigated, gene silencing remains understudied, especially…
The solid diffusive phase transformation involving the nucleation and growth of one nucleus is universal and frequently employed but has not yet been fully understood at the atomic level. Here, our first-principles calculations reveal a…
We give a simple criterion when a Gluck twisting an odd smooth 4-manifold along a 2-sphere $S\subset X$ does not change its diffeomorphism type. We obtain this by handlebody techniques and plug twisting operation, getting a slightly…
High-resolution structural information on membrane proteins is essential for understanding cell biology and for structure-based design of new medical drugs and drug delivery strategies. X-ray diffraction (XRD) can provide {\AA}ngstrom-level…
In computational molecular biology, gene regulatory binding sites prediction in whole genome remains a challenge for the researchers. Now a days, the genome wide regulatory binding site prediction tools required either direct pattern…
This study presents a complete structural and biological characterization of Doxorubicin CaCO3 single crystals as a pH responsive drug carrier. Using a biomimetic approach, it was demonstrated that calcite single crystals are able, during…
The correct description of nondynamic correlation by electronic structure methods not belonging to the multireference family is a challenging issue. The transition of $D_{2h}$ to $D_{4h}$ symmetry in H$_4$ molecule is among the most simple…
X-ray absorption spectroscopy (XAS) is widely employed for structure characterization of graphitic carbon nitride (g-C$_3$N$_4$) and its composites. Nevertheless, even for pure g-C$_3$N$_4$, discrepancies in energy and profile exist across…
Understanding the relationship between protein sequences and their functions is fundamental to protein engineering, but this task is hindered by the combinatorially vast sequence space and the experimental noise inherent in fitness…
The diffusion-controlled limit of reaction times for site-specific DNA-binding proteins is derived from first principles. We follow the generally accepted concept that a protein propagates via two competitive modes, a three-dimensional…
DNA helicases are molecular motors that use the energy from ATP hydrolysis to move along DNA, promoting the unwinding or rewinding of the double helix. Here, we use magnetic and optical tweezers to track the motion of three helicases, gp41,…
The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling $G$ between twisting and bending, known to arise from…
In the present work we study and compare unfolding of a small protein, chicken villin headpiece (HP-36) in two different aqueous binary mixtures, namely water-ethanol (EtOH) and water-dimethyl sulphoxide (DMSO). In both the binary mixtures,…
Using Monte Carlo simulations, we study the hysteresis in unzipping of a double stranded block copolymer DNA with $-A_n B_n-$ repeat units. Here $A$ and $B$ represent two different types of base pairs having two- and three-bonds,…
We present a theoretical study of single-stranded DNA under stretching. Within the proposed framework, the effects of basepairing on the mechanical response of the molecule can be studied in combination with an arbitrary underlying model of…
Deep learning has made significant progress in protein structure prediction, advancing the development of computational biology. However, despite the high accuracy achieved in predicting single-chain structures, a significant number of…