Molecular dynamics simulations play a pivotal role in elucidating the dynamic behaviors of RNA structures, offering valuable complement to traditional methods such as nuclear magnetic resonance or X-ray. Despite this, current precision force fields lags behind that protein fields. In this work, we systematically compared performance four (ff99bsc0χOL3, AMBERDES, ff99OL3_CMAP1, AMBERMaxEnt) across diverse structures. Our findings highlight significant challenges maintaining stability,...

Phosphorylation of proteins plays an important regulatory role at almost all levels cellular organization. Molecular dynamics (MD) simulation is a promising tool to reveal the mechanism how phosphorylation regulates many key biological processes atomistic level. MD accuracy depends on force field precision, while current fields for phospho-amino acids have resulted in notable inconsistency with experimental data. Here, new parameter (named FB18CMAP) generated by fitting against quantum...

Phosphorylated proteins play a crucial role in numerous cellular processes, acting as key regulators signal transduction networks, cell expansion, and various biochemical reactions. Molecular dynamics (MD) simulations are powerful tools for exploring the dynamic conformations of phosphoproteins. However, conventional force fields often underestimate radii gyration (Rg) To address this limitation, we reoptimized parameters vDW radius oxygen atom charge phosphorus with reweighting algorithm...

Machine learning force fields offer the ability to simulate biomolecules with quantum mechanical accuracy while significantly reducing computational costs, attracting a growing amount of attention in biophysics. Meanwhile, by leveraging efficiency molecular mechanics modeling solvent molecules and long-range interactions, hybrid machine learning/molecular (ML/MM) model offers more realistic approach describing complex biomolecular systems solution. However, multiscale models electrostatic...

Excited-ground-state transition and strand slippage of RNA play key roles in transcription translation central dogma. Due to limitation current experimental techniques, the dynamic structure ensembles remain inadequately understood. Molecular dynamics simulations offer a promising complementary approach, whose accuracy depends on force field. Here, we develop new version base-specific field (BSFF2) address underestimation base pairing stability artificial backbone conformations. Extensive...

Due to the tremendous increases in demand for performance based navigation and in-flight broadband Internet access aeronautical industry, Aeronautical Ad-hoc Networks (AANETs) have been deemed as a viable solution provide aircraft-to-aircraft communications without aid of ground stations satellite system. In this paper, we attempt address fundamental concerns arising AANETs, namely, under what conditions AANETs are connected such that end-to-end between aircrafts feasible. We consider on...

Phosphorylation plays a key role in plant biology, such as the accumulation of cells to form observed proteome. Statistical analysis found that many phosphorylation sites are located disordered regions. However, current force fields mainly trained for structural proteins, which might not have capacity perfectly capture dynamic conformation phosphorylated proteins. Therefore, we evaluated performance ff03CMAP, balanced field between and sampling The test results 11 different systems,...

Power line communication technology is one of the power specific functions that can be utilized by grid for real-time monitoring operation status. This paper presents an impedance estimation technique based on to track and predict input use predicted fault identification. Three typical topological network structures are adopted derive results under different impedances. The simulations show well identified, indicating not only monitor in real time, but also identify types faults.

Due to the close relationship between power grid fault and impedance, there is a significant defect in use of line communication (PLC) equipment monitor locate faults, which lack real-time impedance information. Therefore, this study proposes new monitoring method based on estimation equipment. The channel frequency response (CFR) obtained from PLC receiver used estimate high-frequency input ground real time. Firstly, multi-conductor transmission theory, bottom-up modeling technology, basic...

Digital computation on stochastic bit streams is a non-conventional type of computation, which uses digital circuits to process probabilistic inputs. In this paradigm, compute the probability values. This leads extremely simple implementations for complex arithmetic operations. The combinational logic-based designs can be implemented in parallel realize fast by trading off silicon area with delay. However, it impossible implement current sequential reduce delay, since they need large number...

The dynamics of a plane mixing layer as well its noise production are investigated through global mode decomposition the linearized simulation and nonlinear generalization called Koopman mode. Through projection shear onto set modes, we demonstrate significant efficiency in capturing nearand far-field behaviours instability waves. In particular, associated with first subharmonic is dominant acoustic radiation underlying flow dynamics. Within framework, sound generation mechanism...

Promoting acceleration sensitivity of three-dimensional fiber-optic inertial vector hydrophone is an important requirement in underwater acoustic sensing. Firstly, numerical calculating and finite element simulating technologies are both used to study the sensitivity. By simulation, it gets relationship curve between sensing frequency, with work frequency 20Hz-2000Hz 28.7dB designing parameters. Secondly, fabricated using parameters simulation. Finally, a measurement setup built, its tested....

Abstract It is vitally important to identify sources from which unwanted noise and vibration are emitted before further research work can commence on the design optimization of cylindrical cam mechanism. Acoustic microphone accelerometer measurement systems were used analyze system characteristics in both time frequency domains. We have succeeded identifying distinguishing signals between regions groove junctions inversions terms relative values their instantaneous powers. Some problems...