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Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…
Recent advances in high-throughput sequencing technologies have enabled the extraction of multiple features that depict patient samples at diverse and complementary molecular levels. The generation of such data has led to new challenges in…
The spatial positioning of chromosomes relative to functional nuclear bodies is intertwined with genome functions such as transcription. However, the sequence patterns and epigenomic features that collectively influence chromatin spatial…
Characterizing chirality is highly important for applications in the pharmaceutical industry, as well as in the study of dynamical chemical and biological systems. However, this task has remained challenging, especially due to the ongoing…
We use nucleosome maps obtained by high-throughput sequencing to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of…
A computational approach via implementation of the Principle Component Analysis (PCA) and Gaussian Mixture (GM) clustering methods from Machine Learning (ML) algorithms to identify domain structures of supercooled liquids is developed. Raw…
Understanding protein flexibility and its dynamic interactions with other molecules is essential for studying protein function. Although cryogenic electron microscopy(cryo-EM) provides an opportunity to observe macromolecular dynamics…
In equilibrium self-assembly, microscopic building blocks spontaneously self-organize into stable structures as dictated by their interaction potentials, which limits the accessible structural features to those that correspond to global…
To understand the nature of a cell, one needs to understand the structure of its genome. For this purpose, experimental techniques such as Hi-C detecting chromosomal contacts are used to probe the three-dimensional genomic structure. These…
Molecular dynamics (MD) simulations present a data-mining challenge, given that they can generate a considerable amount of data but often rely on limited or biased human interpretation to examine their information content. By not asking the…
Different phoretic driving mechanisms have been proposed for the transport of solid or liquid microscopic inclusions in integrated chemical processes. However, the ability to reversibly address both the flow path, rate, and local reactant…
During interphase, a typical cell nucleus features spatial compartmentalization of transcriptionally active euchromatin and repressed heterochromatin domains. In conventional nuclear organization, euchromatin predominantly occupies the…
The interaction between light and matter can be controlled efficiently by structuring materials at a length scale shorter than the wavelength of interest. With the goal to build optical devices that operate at the nanoscale, plasmonics has…
Coarse-graining offers a means to extend the achievable time and length scales of molecular dynamics simulations beyond what is practically possible in the atomistic regime. Sampling molecular configurations of interest can be done…
We describe a new generation of algorithms capable of mapping the structure and conformations of macromolecules and their complexes from large ensembles of heterogeneous snapshots, and demonstrate the feasibility of determining both…
High-order harmonic generation (HHG) is a powerful tool for probing electronic structure and ultrafast dynamics in matter. Traditionally studied in atomic and molecular gases, HHG has recently been extended to condensed matter, enabling…
High-harmonic generation (HHG) in condensed-matter systems is both a source of fundamental insight into quantum electron motion and a promising candidate to realize compact ultraviolet and ultrafast light sources. Here we argue that the…
Unsupervised cell type identification is crucial for uncovering and characterizing heterogeneous populations in single cell omics studies. Although a range of clustering methods have been developed, most focus exclusively on intrinsic…
A problem of substantial interest is to systematically map variation in chromatin structure to gene expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for…
One of the most important tasks in understanding the complex spatial organization of the genome consists in extracting information about this spatial organization, the function and structure of chromatin topological domains from existing…