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Density functional theory (DFT) has become a standard tool for the study of point defects in materials. However, finding the most stable defective structures remains a very challenging task as it involves the solution of a multimodal…
Despite the wide existence of vesicles in living cells as well as their important applications like drug-delivery, the underlying mechanism of vesicle fusion/fission remains under debate. Here, we develop a constrained self-consistent field…
Superoxide reductase SOR is a non-heme iron metalloenzyme that detoxifies superoxide radical in microorganisms. Its active site consists of an unusual non-heme Fe2+ center in a [His4 Cys1] square pyramidal pentacoordination, with the axial…
Telomeres, the nucleoprotein complexes at the termini of linear chromosomes, are essential for the processes of end replication, end protection, and chromatin segregation. The Mre11 complex is involved in multiple cellular roles in DNA…
Enterotoxigenic Escherichia coli (ETEC) are a major cause of diarrhea worldwide, and infection of children in underdeveloped countries often leads to high mortality rates. Isolated ETEC express a plethora of colonization factors…
The role of post-translational modification of histones in eukaryotic gene regulation is well recognized. Epigenetic silencing of genes via heritable chromatin modifications plays a major role in cell fate specification in higher organisms.…
High-throughput molecular screening is required to investigate the origin and diffusion of antimicrobial resistance in pathogen outbreaks. The most frequent cause of human infection is Escherichia coli, which is dominated by sequence type…
Switch-like motifs are among the basic building blocks of biochemical networks. A common motif that can serve as an ultrasensitive switch consists of two enzymes acting antagonistically on a substrate, one making and the other removing a…
Transforming growth factor beta (TGF$\beta$) plays a central role in morphogenesis, growth, and cell differentiation. This cytokine is particularly important in cartilage where it regulates cell proliferation and extracellular matrix…
Pathogenic enterotoxigenic Escherichia coli (ETEC) are the major bacterial cause of diarrhea in young children in developing countries and in travelers, causing significant mortality in children. Adhesive fimbriae are a prime virulence…
DNA methylation is a primary layer of epigenetic modification that plays a pivotal role in the regulation of development, aging, and cancer. The concurrent activity of opposing enzymes that mediate DNA methylation and demethylation gives…
Proteins are only moderately stable. It has long been debated whether this narrow range of stabilities is solely a result of neutral drift towards lower stability or purifying selection against excess stability is also at work - for which…
The accumulation of adaptive mutations is essential for survival in novel environments. However, in clonal populations with a high mutational supply, the power of natural selection is expected to be limited. This is due to clonal…
A new computational scheme to analyze electron transfer (ET) pathways in large biomolecules is presented with applications to ETs in bacterial photosynthetic reaction center. It consists of a linear combination of fragment molecular…
Culturing cells confined in microscale geometries has been reported in many studies this last decade, in particular following the development of microfluidic-based applications and lab-on-a-chip devices. Such studies usually examine growth…
Even closely related prokaryotes show an astounding diversity in their ability to grow in different nutritional environments. Mechanistically, this diversity arises predominantly through horizontal gene transfer, the exchange of DNA between…
We report on the synthesis, STM imaging and theoretical studies of the structure, electronic structure and transport properties of linear chains of styrene and methyl-styrene molecules and their heterojunctions on hydrogen-terminated…
Escherichia coli and Bacillus subtilis are two of the best-studied prokaryotic model organisms. Previous analyses of their transcriptional regulatory networks have shown that they exhibit high plasticity during evolution and suggested that…
The exploration of solid-solid phase transition suffers from the uncertainty of how atoms in two crystal structures match. We devised a theoretical framework to describe and classify crystal-structure matches (CSM). Such description fully…
The catalytic properties of Pt2XSe3 (X = Hg, Zn) in hydrogen-electrode- (HER-) based catalysts have been investigated based on state-of-the-art ab initio simulations. Our results show that the late transition metal sites (Hg and Zn) exhibit…