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The recent improvements in cryo-electron microscopy (cryo-EM) in the past few years are now allowing to observe molecular complexes at atomic resolution. As a consequence, numerous structures derived from cryo-EM are now available in the…
We use a neural network model and ALMA observations of HCN and HNC to constrain the physical conditions, most notably the cosmic-ray ionization rate (CRIR, zeta), in the Central Molecular Zone (CMZ) of the starburst galaxy NGC 253. Using…
We investigate the mechanical stability of a segment of DNA wrapped around a histone in the nucleosome configuration. The assumption underlying this investigation is that the proper model for this packaging arrangement is that of an elastic…
To test whether X-chromosome has unique genomic characteristics, X-chromosome and 22 autosomes were compared for RNA binding density. Nucleotide sequences on the chromosomes were divided into 50kb per segment that was recoded as a set of…
We report on our calculations of the inner-sphere reorganization energy and the interaction of the pi orbitals within DNA oligomers. The exponential decrease of the electronic coupling between the highest and second highest occupied base…
The unconstrained genomic DNA of bacteria forms a coil, which volume exceeds 1000 times the volume of the cell. Since prokaryotes lack a membrane-bound nucleus, in sharp contrast with eukaryotes, the DNA may consequently be expected to…
We propose a new regularization scheme to study the bound state of two-nucleon systems in Lattice Effective Field Theory. Inspired by continuum EFT calculation, we study an exponential regulator acting on the leading-order (LO) and…
Living systems contain intricate biochemical networks whose structure is closely related to their function and allows them to exhibit robust behavior in the presence of external stimuli. Such networks typically involve catalytic enzymes,…
Lattice reduction is a popular preprocessing strategy in multiple-input multiple-output (MIMO) detection. In a quest for developing a low-complexity reduction algorithm for large-scale problems, this paper investigates a new framework…
Single molecule experiments on single- and double stranded DNA have sparked a renewed interest in the force-extension of polymers. The extensible Freely Jointed Chain (FJC) model is frequently invoked to explain the observed behavior of…
The three exceptional lattices, $E_6$, $E_7$, and $E_8$, have attracted much attention due to their anomalously dense and symmetric structures which are of critical importance in modern theoretical physics. Here, we study the electronic…
Motivation: High-coverage sequencing data have significant, yet hard to exploit, redundancy. Most FASTQ compressors cannot efficiently compress the DNA stream of large datasets, since the redundancy between overlapping reads cannot be…
Many proteins interact with and deform double-stranded DNA in cells. Single-molecule experiments have studied the elasticity of DNA with helix-deforming proteins, including proteins that bend DNA. These experiments increase the need for…
Experimental evidence lends support to the conjecture that the ability of chains of cells to sense the gradient of an external chemical concentration could rely on cell-to-cell communication. This is the basis for the gradient sensing…
The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent…
The epitaxial growth of complex oxides enables the production of high-quality films, yet substrate choice is restricted to certain symmetry and lattice parameters, thereby limiting the technological applications of epitaxial oxides. In…
Bacterial chemotactic sensing converts noisy chemical signals into running and tumbling. We analyze the static sensing limits of mixed Tar/Tsr chemoreceptor clusters in individual Escherichia coli cells using a heterogeneous…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
We study the problem of compression for the purpose of similarity identification, where similarity is measured by the mean square Euclidean distance between vectors. While the asymptotical fundamental limits of the problem - the minimal…
The DNA storage channel is considered, in which the $M$ Deoxyribonucleic acid (DNA) molecules comprising each codeword are stored without order, sampled $N$ times with replacement, and then sequenced over a discrete memoryless channel. For…