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The identification of cellular objectives is one of the central topics in the research of microbial metabolic networks. In particular, the information about a cellular objective is needed in flux balance analysis which is a commonly used…
Rapid changes in extracellular osmolarity are one of many insults microbial cells face on a daily basis. To protect against such shocks, Escherichia coli and other microbes express several types of transmembrane channels which open and…
Background: Previous studies have used different methods in an effort to extract the modular organization of transcriptional regulatory networks (TRNs). However, these approaches are not natural, as they try to cluster highly connected…
Adaptation of the chemotaxis sensory pathway of the bacterium Escherichia coli is integral for detecting chemicals over a wide range of background concentrations, ultimately allowing cells to swim towards sources of attractant and away from…
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…
Epithelial-Mesenchymal Transition (EMT), and the corresponding reverse process, Mesenchymal-Epithelial Transition (MET), are dynamic and reversible cellular programs orchestrated by many changes at biochemical and morphological levels. A…
Over the last two decades epidermal growth factor receptor (EGFR) kinase has become an important target to treat non-small cell lung cancer (NSCLC). Currently, three generations of EGFR kinase-targeted small molecule drugs have been FDA…
Due to the permanent harm to human health and ecosystem balance, antibiotic pollution in water has become an important direction of current environmental governance. Spherical metal oxides (SMOs) have been frequently utilized as effective…
We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the…
Single-atom catalysts are considered as a promising method for efficient energy conversion, owing to their advantages of high atom utilization and low catalyst cost. However, finding a stable two-dimensional structure and high hydrogen…
We unravel how functional plasticity and redundancy are essential mechanisms underlying the ability to survive of metabolic networks. We perform an exhaustive computational screening of synthetic lethal reaction pairs in Escherichia coli in…
Subunit epsilon is an intrinsic regulator of the bacterial FoF1-ATP synthase, the ubiquitous membrane-embedded enzyme that utilizes a proton motive force in most organisms to synthesize adenosine triphosphate (ATP). The C-terminal domain of…
The goal of this dissertation is to study the sequence polymorphism in retrotransposable elements of Entamoeba histolytica. The Quasispecies theory, a concept of equilibrium (stationary), has been used to understand the behaviour of these…
Bacterial growth environment strongly influences the efficacy of antibiotic treatment, with slow growth often being associated with decreased susceptibility. Yet in many cases the connection between antibiotic susceptibility and pathogen…
Molybdenum disulfide (MoS$_2$) is a prototypical layered transition-metal dichalcogenide whose electrocatalytic performance is governed by a delicate balance between crystallinity, defect density, and electronic conductivity. Here we report…
In this study, we synthesized S functionalized graphene sponge electrode and applied it for electrochemical oxidation of five commonly used antibiotics, namely sulfamethoxazole, trimethoprim, ofloxacin, roxithromycin and erythromycin, and…
We demonstrate that cyclooctatetraene (COT) can be stabilised in different conformations when adsorbed on different noble-metal surfaces due to varying molecule-substrate interaction. While at first glance the behaviour seems to be in…
Bacterial chemotaxis for E.coli is controlled by methylation of chemoreceptors, which in a biochemical pathway regulates the concentration of the CheY-P protein that finally controls the tumbling rate. As a consequence, the tumbling rate…
Chemotaxis of the bacterium Escherichia coli is well understood in shallow chemical gradients, but its swimming behavior remains difficult to interpret in steep gradients. By focusing on single-cell trajectories from simulations, we…
Bone marrow stromal cells (BMSC) -- which include skeletal stem cells -- are a promising tool in regenerative medicine. However, their heterogeneous and unpredictable in vivo behaviour remains a critical barrier preventing the development…