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While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
We study the Brownian dynamics of a solid particle on a vibrating solid surface. Phenomenologically, the interaction between the two solid surfaces is modeled by solid friction, and the Gaussian white noise models the vibration of the solid…
Time-domain Brillouin scattering uses ultrashort laser pulses to generate coherent acoustic pulses of picoseconds duration in a solid sample and to follow their propagation in order to image material inhomogeneities with sub-optical depth…
Crystal structures of simple metals and binary alloy phases based on the close-packed hexagonal structure are analyzed within the model of Fermi sphere-Brillouin zone interactions to understand distortions and superlattices. Examination of…
Principal component analysis (PCA) plays an important role in the analysis of cryo-EM images for various tasks such as classification, denoising, compression, and ab-initio modeling. We introduce a fast method for estimating a compressed…
Understanding the structure of a protein complex is crucial indetermining its function. However, retrieving accurate 3D structures from microscopy images is highly challenging, particularly as many imaging modalities are two-dimensional.…
Brillouin microscopy is an emerging optical elastography technique that can be used to assess mechanical properties of biological samples in a 3D, all-optical and hence non-contact fashion. However, the low cross-section of spontaneous…
When nanoparticles (NPs) are introduced into a biological solution, layers of biomolecules form on their surface, creating a corona. Understanding how the structure of the protein evolves into the corona is essential for evaluating the…
Molecular surface representations have been advertised as a great tool to study protein structure and functions, including protein-ligand binding affinity modeling. However, the conventional surface-area-based methods fail to deliver a…
Here we introduce three-dimensional single-shot ptychography (3DSSP). 3DSSP leverages an additional constraint unique to the single-shot geometry to deconvolve multiple 2D planes of a 3D object. Numeric simulations and analytic calculations…
Cryo-electron microscopy (Cryo-EM) enables high-resolution imaging of biomolecules, but structural heterogeneity remains a major challenge in 3D reconstruction. Traditional methods assume a discrete set of conformations, limiting their…
Delivering sub-micrometer particles to an intense x-ray focus is a crucial aspect of single-particle diffractive-imaging experiments at x-ray free-electron lasers. Enabling direct visualization of sub-micrometer aerosol particle streams…
Enzymes have been shown to diffuse faster in the presence of their reactants. Recently, we revealed new insights into this process of enhanced diffusion using single-particle tracking (SPT) with total internal reflection fluorescence (TIRF)…
A colloidal suspension of active Brownian particles (ABPs) driven by controllable forces into directed or persistent motions can serve as a model for understanding the biological systems. Experiments and numerical simulations are…
The development of many optical quantum technologies depends on the availability of solid-state single quantum emitters with near-perfect optical coherence. However, a standing issue that limits systematic improvement is the significant…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
Protein design is the inverse approach of the three-dimensional (3D) structure prediction for elucidating the relationship between the 3D structures and amino acid sequences. In general, the computation of the protein design involves a…
Understanding complex biological macromolecules, especially proteins, is vital for grasping their diverse chemical functions with direct impact in biology and pharmacology. While techniques like X-ray crystallography and cryo-electron…
A protein is a linear chain containing a set of amino acids, which folds on itself to create a specific native structure, also called the minimum energy conformation. It is the native structure that determines the functionality of each…
We reconstruct a 3D model of the surface of a material undergoing fatigue testing and experiencing cracking. Specifically we reconstruct the surface depth (out of plane intrusions and extrusions) and lateral (in-plane) motion from multiple…