相关论文: ATP Hysteresis in Tripartite Synapses
Here we generalize our previous model of molecular motors trafficking subdiffusing cargos in viscoelastic cytosol by (i) including mechanochemical coupling between cyclic conformational fluctuations of the motor protein driven by the…
We studied autoassociative networks in which synapses are noisy on a time scale much shorter that the one for the neuron dynamics. In our model a presynaptic noise causes postsynaptic depression as recently observed in neurobiological…
Absorbing phase transitions (APTs) are widespread in non-equilibrium systems, spanning condensed matter, epidemics, earthquakes, ecology, and chemical reactions. APTs feature an absorbing state in which the system becomes entrapped, along…
Multistability-induced hysteresis has been widely studied in mechanical systems, but such behavior has proven more difficult to reproduce experimentally in flow networks. Natural flow networks like animal and plant vasculature can exhibit…
Memories are stored, at least partly, as patterns of strong synapses. Given molecular turnover, how can synapses maintain strong for the years that memories can persist? Some models postulate that biochemical bistability maintains strong…
The rational development of specific inhibitors for the ~500 protein kinases encoded in the human genome is impeded by a poor understanding of the structural basis for the activity and selectivity of small molecules that compete for ATP…
Intrinsic transcriptional noise induced by operator fluctuations is investigated with a simple spin like stochastic model. The effects of transcriptional fluctuations in protein synthesis is probed by coupling transcription and translation…
Expressing the energy content of food as the heat energy released by its combustion is potentially misleading. Food is used to produce adenosine triphosphate (ATP). The free energy of conversion of ATP into adenosine diphosphate is used…
The mitogen-activated protein kinase (MAPK) signaling cascade, an evolutionarily conserved motif present in all eukaryotic cells, is involved in coordinating critical cell-fate decisions, regulating protein synthesis, and mediating learning…
Neuronal networking supports complex brain functions, with neurotransmitters facilitating communication through chemical synapses. The release probability of neurotransmitters varies and is influenced by pre-synaptic neuronal activity.…
Thixotropy, anti-thixotropy, and viscoelasticity are three types of time-dependent dynamics that involve fundamentally different underlying physical processes. Yet distinguishing them can be very challenging, which hinders the understanding…
The studies described in this dissertation have attempted to address the cellular mechanisms of information storage by the brain. My work has focused primarily on the postsynaptic events that occur during and after induction of long-term…
Spike Timing Dependent Plasticity (STDP) is a Hebbian like synaptic learning rule. The basis of STDP has strong experimental evidences and it depends on precise input and output spike timings. In this paper we show that under biologically…
The framework of bipartite stochastic thermodynamics is a powerful tool to analyze a composite system's internal thermodynamics. It has been used to study the components of different molecular machines such as ATP synthase. However, this…
Neurotensin receptor 1 (NTSR1), a member of the Class A G protein-coupled receptor superfamily, plays an important role in modulating dopaminergic neuronal activity and eliciting opioid-independent analgesia. Recent studies suggest that…
p27$^{Kip1}$ (p27) is an intrinsically disordered protein (IDP) that folds upon binding to cyclin-dependent kinase (Cdk)$/$cyclin complexes (e.g., Cdk2$/$cyclin A), inhibiting their catalytic activity and causing cell cycle arrest. However,…
RNA polymerase (RNAP) is molecular machine that polymerizes a RNA molecule, a linear heteropolymer, using a single stranded DNA (ssDNA) as the corresponding template; the sequence of monomers of the RNA is dictated by that of monomers on…
Adenosine triphosphate (ATP) is the universal chemical energy currency for cellular activities provided mainly by the membrane enzyme FoF1-ATP synthase in bacteria, chloroplasts and mitochondria. Synthesis of ATP is accompanied by subunit…
Both genomic stability and sustenance of day-to-day life rely on efficient and accurate readout of the genetic code. Single-molecule experiments show that transcription and replication are highly stochastic and irregular processes, with the…
Immune cells recognize and discriminate antigens through immunological synapses - dynamic intercellular junctions exhibiting highly organized receptor-ligand patterns. While much work has focused on molecular kinetics and passive mechanisms…