2,614 research outputs found
Study of Balance Equations for Hot-Electron Transport in an Arbitrary Energy Band (III)
By choosing an electron gas resting instead of drifting in the laboratory
coordinate system as the initial state, the first order perturbation
calculation of the previous paper (Phys. Stat. Sol. (b) 198, 785(1996)) is
revised and extended to include the high order field corrections in the
expression for the frictional forces and the energy transfer rates. The final
expressions are formally the same as those in first order in the electric
field, but the distribution functions of electrons appearing in them are
defined by different expressions. The problems relative to the distribution
function are discussed in detail and a new closed expression for the
distribution function is obtained. The nonlinear impurity-limited resistance of
a strong degenerate electron gas is computed numerically. The result calculated
by using the new expression for the distribution function is quite different
from that using the displaced Fermi function when the electric field is
sufficiently high.Comment: 15 pages with 3 PS figures, RevTeX, to be published in Physica Status
Solidi (b
Molecular docking via quantum approximate optimization algorithm
Molecular docking plays a pivotal role in drug discovery and precision
medicine, enabling us to understand protein functions and advance novel
therapeutics. Here, we introduce a potential alternative solution to this
problem, the digitized-counterdiabatic quantum approximate optimization
algorithm (DC-QAOA), which utilizes counterdiabatic driving and QAOA on a
quantum computer. Our method was applied to analyze diverse biological systems,
including the SARS-CoV-2 Mpro complex with PM-2-020B, the DPP-4 complex with
piperidine fused imidazopyridine 34, and the HIV-1 gp120 complex with
JP-III-048. The DC-QAOA exhibits superior performance, providing more accurate
and biologically relevant docking results, especially for larger molecular
docking problems. Moreover, QAOA-based algorithms demonstrate enhanced hardware
compatibility in the noisy intermediate-scale quantum era, indicating their
potential for efficient implementation under practical docking scenarios. Our
findings underscore quantum computing's potential in drug discovery and offer
valuable insights for optimizing protein-ligand docking processes.Comment: 10 pages, 5 figures, All comments are welcom
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A Targeted Quantitative Proteomic Method Revealed a Substantial Reprogramming of Kinome during Melanoma Metastasis.
Kinases are involved in numerous critical cell signaling processes, and dysregulation in kinase signaling is implicated in many types of human cancers. In this study, we applied a parallel-reaction monitoring (PRM)-based targeted proteomic method to assess kinome reprogramming during melanoma metastasis in three pairs of matched primary/metastatic human melanoma cell lines. Around 300 kinases were detected in each pair of cell lines, and the results showed that Janus kinase 3 (JAK3) was with reduced expression in the metastatic lines of all three pairs of melanoma cells. Interrogation of The Cancer Genome Atlas (TCGA) data showed that reduced expression of JAK3 is correlated with poorer prognosis in melanoma patients. Additionally, metastatic human melanoma cells/tissues exhibited diminished levels of JAK3 mRNA relative to primary melanoma cells/tissues. Moreover, JAK3 suppresses the migration and invasion of cultured melanoma cells by modulating the activities of matrix metalloproteinases 2 and 9 (MMP-2 and MMP-9). In summary, our targeted kinome profiling method provided by far the most comprehensive dataset for kinome reprogramming associated with melanoma progression, which builds a solid foundation for examining the functions of other kinases in melanoma metastasis. Moreover, our results reveal a role of JAK3 as a potential suppressor for melanoma metastasis
ACT-GAN: Radio map construction based on generative adversarial networks with ACT blocks
The radio map, serving as a visual representation of electromagnetic spatial
characteristics, plays a pivotal role in assessment of wireless communication
networks and radio monitoring coverage. Addressing the issue of low accuracy
existing in the current radio map construction, this paper presents a novel
radio map construction method based on generative adversarial network (GAN) in
which the Aggregated Contextual-Transformation (AOT) block, Convolutional Block
Attention Module (CBAM), and Transposed Convolution (T-Conv) block are applied
to the generator, and we name it as ACT-GAN. It significantly improves the
reconstruction accuracy and local texture of the radio maps. The performance of
ACT-GAN across three different scenarios is demonstrated. Experiment results
reveal that in the scenario without sparse discrete observations, the proposed
method reduces the root mean square error (RMSE) by 14.6% in comparison to the
state-of-the-art models. In the scenario with sparse discrete observations, the
RMSE is diminished by 13.2%. Furthermore, the predictive results of the
proposed model show a more lucid representation of electromagnetic spatial
field distribution. To verify the universality of this model in radio map
construction tasks, the scenario of unknown radio emission source is
investigated. The results indicate that the proposed model is robust radio map
construction and accurate in predicting the location of the emission source.Comment: 11 pages, 10 figure
Combinatorial optimization problems in self-assembly
Self-assembly is the ubiquitous process by which simple objects autonomously assemble into intricate complexes. It has been suggested that intricate self-assembly processes will ultimately be used in circuit fabrication, nano-robotics, DNA computation, and amorphous computing. In this paper, we study two combinatorial optimization problems related to efficient self-assembly of shapes in the Tile Assembly Model of self-assembly proposed by Rothemund and Winfree [18]. The first is the Minimum Tile Set Problem, where the goal is to find the smallest tile system that uniquely produces a given shape. The second is the Tile Concentrations Problem, where the goal is to decide on the relative concentrations of different types of tiles so that a tile system assembles as quickly as possible. The first problem is akin to finding optimum program size, and the second to finding optimum running time for a "program" to assemble the shape.Self-assembly is the ubiquitous process by which simple objects autonomously assemble into intricate complexes. It has been suggested that intricate self-assembly processes will ultimately be used in circuit fabrication, nano-robotics, DNA computation, and amorphous computing. In this paper, we study two combinatorial optimization problems related to efficient self-assembly of shapes in the Tile Assembly Model of self-assembly proposed by Rothemund and Winfree [18]. The first is the Minimum Tile Set Problem, where the goal is to find the smallest tile system that uniquely produces a given shape. The second is the Tile Concentrations Problem, where the goal is to decide on the relative concentrations of different types of tiles so that a tile system assembles as quickly as possible. The first problem is akin to finding optimum program size, and the second to finding optimum running time for a "program" to assemble the shape. We prove that the first problem is NP-complete in general, and polynomial time solvable on trees and squares. In order to prove that the problem is in NP, we present a polynomial time algorithm to verify whether a given tile system uniquely produces a given shape. This algorithm is analogous to a program verifier for traditional computational systems, and may well be of independent interest. For the second problem, we present a polynomial time -approximation algorithm that works for a large class of tile systems that we call partial order systems
Correlation Analysis for Protein Evolutionary Family Based on Amino Acid Position Mutations and Application in PDZ Domain
BACKGROUND: It has been widely recognized that the mutations at specific directions are caused by the functional constraints in protein family and the directional mutations at certain positions control the evolutionary direction of the protein family. The mutations at different positions, even distantly separated, are mutually coupled and form an evolutionary network. Finding the controlling mutative positions and the mutative network among residues are firstly important for protein rational design and enzyme engineering. METHODOLOGY: A computational approach, namely amino acid position conservation-mutation correlation analysis (CMCA), is developed to predict mutually mutative positions and find the evolutionary network in protein family. The amino acid position mutative function, which is the foundational equation of CMCA measuring the mutation of a residue at a position, is derived from the MSA (multiple structure alignment) database of protein evolutionary family. Then the position conservation correlation matrix and position mutation correlation matrix is constructed from the amino acid position mutative equation. Unlike traditional SCA (statistical coupling analysis) approach, which is based on the statistical analysis of position conservations, the CMCA focuses on the correlation analysis of position mutations. CONCLUSIONS: As an example the CMCA approach is used to study the PDZ domain of protein family, and the results well illustrate the distantly allosteric mechanism in PDZ protein family, and find the functional mutative network among residues. We expect that the CMCA approach may find applications in protein engineering study, and suggest new strategy to improve bioactivities and physicochemical properties of enzymes
Accurate prediction of protein function using statistics-informed graph networks
Understanding protein function is pivotal in comprehending the intricate mechanisms that underlie many crucial biological activities, with far-reaching implications in the fields of medicine, biotechnology, and drug development. However, more than 200 million proteins remain uncharacterized, and computational efforts heavily rely on protein structural information to predict annotations of varying quality. Here, we present a method that utilizes statistics-informed graph networks to predict protein functions solely from its sequence. Our method inherently characterizes evolutionary signatures, allowing for a quantitative assessment of the significance of residues that carry out specific functions. PhiGnet not only demonstrates superior performance compared to alternative approaches but also narrows the sequence-function gap, even in the absence of structural information. Our findings indicate that applying deep learning to evolutionary data can highlight functional sites at the residue level, providing valuable support for interpreting both existing properties and new functionalities of proteins in research and biomedicine
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