A5032386889- Gene Regulatory Network Analysis
- Evolution and Genetic Dynamics
- Microbial Metabolic Engineering and Bioproduction
- Nonlinear Dynamics and Pattern Formation
- Complex Network Analysis Techniques
- Bioinformatics and Genomic Networks
- RNA Research and Splicing
- thermodynamics and calorimetric analyses
- Theoretical and Computational Physics
- Cancer Genomics and Diagnostics
- Enzyme Catalysis and Immobilization
- Chromosomal and Genetic Variations
- Experimental Behavioral Economics Studies
- Biofuel production and bioconversion
- Spectroscopy and Quantum Chemical Studies
- Microbial Community Ecology and Physiology
- Molecular Communication and Nanonetworks
- RNA and protein synthesis mechanisms
- Ion-surface interactions and analysis
- Game Theory and Applications
- Gut microbiota and health
- Diet and metabolism studies
- Stochastic processes and statistical mechanics
- Protein Structure and Dynamics
- Vibrio bacteria research studies
Ulsan National Institute of Science and Technology
2013-2024
Asia Pacific Center for Theoretical Physics
2024
The Ohio State University
2016
Lawrence Livermore National Laboratory
2008-2009
Seoul National University
2002-2005
Abstract Why metalloenzymes often show dramatic changes in their catalytic activity when subjected to chemically similar but non-native metal substitutions is a long-standing puzzle. Here, we report on the roles of ions model metalloenzyme system, human carbonic anhydrase II (CA II). Through comparative study intermediate states zinc-bound native CA and metal-substituted IIs, demonstrate that characteristic ion coordination geometries (tetrahedral for Zn 2+ , tetrahedral octahedral...
Current technological revolutions, involving artificial intelligence, mRNA vaccines, and quantum computing, are largely driven by industry. Despite the existing perception that commercial motives promote cutting-edge innovation, concerns may arise about their risk of limiting scientific exploration from diverse perspectives, which nurtures long-term innovative potential. Here, we investigate interplay between industrial influence analyzing 20 million papers US, Chinese, European patents in...
Intelligent soft matter stands at the intersection of materials science, physics, and cognitive promising to change how we design interact with materials. This transformative field seeks create that possess life-like capabilities, such as perception, learning, memory, adaptive behavior. Unlike traditional materials, which typically perform static or predefined functions, intelligent dynamically interacts its environment. It integrates multiple sensory inputs, retains experiences, makes...
We investigate the kinetic roughening of ${\mathrm{Ar}}^{+}$ ion-sputtered Pd(001) surface both experimentally and theoretically. In situ real-time x-ray reflectivity in scanning tunneling microscopy show that nanoscale adatom islands form grow with increasing sputter time $t$. Surface roughness $W(t)$ lateral correlation length $\ensuremath{\xi}(t)$ follow scaling laws $W(t)\ensuremath{\sim}{t}^{\ensuremath{\beta}}$ $\ensuremath{\xi}(t)\ensuremath{\sim}{t}^{1/z}$ exponents...
A mutator is an allele that increases the mutation rate throughout genome by disrupting some aspect of DNA replication or repair. Mutators increase order 100-fold have been observed to spontaneously emerge and achieve high frequencies in natural populations long-term laboratory evolution experiments with Escherichia coli. In principle, fixation alleles limited (i) competition mutations wild-type backgrounds, (ii) additional deleterious mutational load, (iii) random genetic drift. Using a...
Abstract We evaluated the bactericidal activity of Bdellovibrio bacteriovorus , strain HD100, within blood sera against bacterial strains commonly associated with bacteremic infections, including E. coli, Klebsiella pneumoniae and Salmonella enterica . Tests show that B. HD100 is not susceptible to serum complement or its activity. After a two hour exposure human sera, prey populations decreased 15- 7,300-fold due while, in contrast, population showed loss only 33%. Dot blot analyses this...
Abstract The role of our gut microbiota in health and disease is largely attributed to the collective metabolic activities inhabitant microbes. A system-level framework microbial community structure, mediated through metabolite transport, would provide important insights into complex microbe-microbe host-microbe chemical interactions. This framework, if adaptable both mouse human systems, be useful for mechanistic interpretations vast amounts experimental data from microbiomes murine animal...
Gene expression in a cell entails random reaction events occurring over disparate time scales. Thus, molecular noise that often results phenotypic and population-dynamic consequences sets fundamental limit to biochemical signaling. While there have been numerous studies correlating the architecture of cellular networks with tolerance, only limited effort has made understand dynamic role protein-protein interactions. We developed fully stochastic model for positive feedback control single...
Despite stochastic fluctuations, some genetic switches are able to retain their expression states through multiple cell divisions, providing epigenetic memory. We propose a novel rationale for tuning the functional stability of simple synthetic gene switch protein dimerization. Introducing an approximation scheme access long-time dynamics multiple-component circuits, we find that spontaneous switching rate may exhibit greater than 8 orders magnitude variation. The manipulation circuit's...
The current challenges faced in the development of advanced biofuels from cellulosic biomass include inefficiency recombinant hosts to hydrolyze lignocellulose, incomplete utilization multiple sugars due presence carbon-catabolite repression, lack suitable gene-expression systems for coordinating multiple-gene expression, difficulties optimizing a synthetic metabolic pathway and toxicity both substrate (lignin) end product (biofuel) host. Despite aforementioned hurdles, potential such as...
A Reply to the Comment by Barthélemy.Received 30 May 2003DOI:https://doi.org/10.1103/PhysRevLett.91.189804©2003 American Physical Society
Examples of heterozygote advantage in humans are scarce and limited to protein-coding sequences. Here, we attempt a genome-wide functional inference advantageous heterozygosity at cis-regulatory regions.The single-nucleotide polymorphisms bearing the signatures balancing selection enriched active regions immune cells epithelial cells, latter which provide barrier function innate immunity. associated with ancient trans-specific also discovered. Allelic imbalance chromatin accessibility...
Circadian protein oscillations are maintained by the lifelong repetition of production and degradation in daily balance. It comes at cost ever-replayed, futile synthesis each day. This biosynthetic with a given oscillatory profile is relievable rhythmic, not constant, rate that selectively peaks right time day but remains low elsewhere, saving much gross loss replenishing synthesis. Here, our mathematical modeling reveals rhythmic proteins circadian spontaneously emerges under steady limited...
Starting with the first publication of lacZ gene fusion in 1980, reporter genes have just entered their fourth decade. Initial studies relied on simple a promoter or particular interest. Such constructs were then used to determine activity under specific conditions within given cell organ. Although this protocol was, and still is, very effective, current research shows paradigm shift has occurred use systems. With advent innovative cloning synthetic biology techniques...
The Michaelis-Menten (MM) rate law has been the dominant paradigm of modeling biochemical processes for over a century with applications in biochemistry, biophysics, cell biology, systems and chemical engineering. MM its remedied form stand on assumption that concentration complex interacting molecules, at each moment, approaches an equilibrium (quasi-steady state) much faster than molecular concentrations change. Yet, this is not always justified. Here, we relax quasi-steady state...