THE DYNAMIC PROPERTIES FOR THE PROTEIN MOLECULAR SYSTEM

In this paper, a new theory for the dynamic properties of protein molecular system have been proposed by means of the analysis of the characteristics of the collective excitations generated under the localized fluctuation and the deformation of structure of the protein. Some new results obtained from this study show that the Davydov theory is an approximate and disadvantegeous theory.

Impact of Vibration Models on Heat Capacities of HF Molecular System

Based on the analysis of completeness and finiteness of HF molecular vibrational levels, HF systemic vibrational heat capacity is studied with quantum statistical and full set of vibrational energy level determined AM (algebraic method). The results show that correct vibrational description and vibrational energy level set of HF system are key factors in calculating heat capacity, HF heat capacity data determined by AM energy spectra {Eυ} are much superior to the ones of harmonic oscillator model, AM results are agreement with experiment data.

Geometrodynamical Analysis to Characterize the Dynamics and Stability of a Molecular System through the Boundary of the Hill’s Region

In this paper we study the dynamics and stability of a two-dimensional model for the vibrations of the LiCN molecule making use of the Riemannian geometry via the Jacobi-Levi-Civita equations applied to the Jacobi metric. The Stability Geometrical Indicator for short times is calculated to locate regular and chaotic trajectories as the relative extrema of this indicator. Only trajectories with initial conditions at the boundary of the Hill’s region are considered to characterize the dynamics of the system. The importance of the curvature of this boundary for the stability of trajectories bouncing on it is also discussed.

The Exploration of Trimeresurus Divided to Multiple Genera Based on Molecular Systematics

According to the contradictions about classification on Trimeresurus between ＂China＇s Fauna＂ and international database, the rationality about Trimeresurus divided to multiple genera based on molecular systematies was discussed. The genetic distance was calculated by sequencing 12S gene of the original Trimeresurus snakes, including 80 individuals of 33 species ; and the molecular phylogenetie tree was established by taking Hypnale hypnale as the outgroup. The results showed that the topological structures of ME tree and ML tree were basically consistent, and all of the species in the molecular trees were divided into 8 branches; and the difference of T. albolabris between Hainan and other locations is not obvious. The viewpoint that original Trimeresurus genera subdivided into 8 genera was more rational, and new authoritative reference books are expected to be published in China.

Do GMOs Accumulate Formaldehyde and Disrupt Molecular Systems Equilibria? Systems Biology May Provide Answers

Safety assessment of genetically modified organisms (GMOs) is a contentious topic. Proponents of GMOs assert that GMOs are safe since the FDA’s policy of substantial equivalence considers GMOs “equivalent” to their non-GMO counterparts, and argue that genetic modification (GM) is simply an extension of a “natural” process of plant breeding, a form of “genetic modification”, though done over longer time scales. Anti-GMO activists counter that GMOs are unsafe since substantial equivalence is unscientific and outdated since it originates in the 1970s to assess safety of medical devices, which are not comparable to the complexity of biological systems, and contend that targeted GM is not plant breeding. The heart of the debate appears to be on the methodology used to determine criteria for substantial equivalence. Systems biology, which aims to understand complexity of the whole organism, as a system, rather than just studying its parts in a reductionist manner, may provide a framework to determine appropriate criteria, as it recognizes that GM, small or large, may affect emergent properties of the whole system. Herein, a promising computational systems biology method couples known perturbations on five biomolecules caused by the CP4 EPSPS GM of Glycine max L. (soybean), with an integrative model of C1 metabolism and oxidative stress (two molecular systems critical to plant function). The results predict significant accumulation of formaldehyde and concomitant depletion of glutathione in the GMO, suggesting how a “small” and single GM creates “large” and systemic perturbations to molecular systems equilibria. Regulatory agencies, currently reviewing rules for GMO safety, may wish to adopt a systems biology approach using a combination of in silico, computational methods used herein, and subsequent targeted experimental in vitro and in vivo designs, to develop a systems understanding of “equivalence” using biomarkers, such as formaldehyde and glutathione, which predict metabolic disruptions, towards modernizing the safety assessment of GMOs.

The chemical environment and structural ordering in liquid Mg-Y-Zn system:An ab-initio molecular dynamics investigation of melt for the formation mechanism of LPSO structure

In an effort to clarify the formation mechanism of LPSO structure in Mg-Y-Zn alloy,the chemical environment and structural ordering in liquid Mg-rich Mg-Y-Zn system are investigated with the aid of ab-initio molecular dynamics simulation.In liquid Mg-rich Mg-Y alloys,the strong Mg-Y interaction is determined,which promotes the formation of fivefold symmetric local structure.For Mg-Zn alloys,the weak Mg-Zn interaction results in the fivefold symmetry weakening in the liquid structure.Due to the coexistence of Y and Zn,the strong attractive interaction is introduced in liquid Mg-Y-Zn ternary alloy,and contributes to the clustering of Mg,Y,Zn launched from Zn.What is more,the distribution of local structures becomes closer to that in pure Mg compared with that in binary Mg-Y and Mg-Zn alloys.These results should relate to the origins of the Y/Zn segregation zone and close-packed stacking mode in LPSO structure,which provides a new insight into the formation mechanism of LPSO structure at atomic level.

A Real-time Prediction System for Molecular-level Information of Heavy Oil Based on Machine Learning

Acquiring accurate molecular-level information about petroleum is crucial for refining and chemical enterprises to implement the“selection of the optimal processing route”strategy.With the development of data prediction systems represented by machine learning,it has become possible for real-time prediction systems of petroleum fraction molecular information to replace analyses such as gas chromatography and mass spectrometry.However,the biggest difficulty lies in acquiring the data required for training the neural network.To address these issues,this work proposes an innovative method that utilizes the Aspen HYSYS and full two-dimensional gas chromatography-time-of-flight mass spectrometry to establish a comprehensive training database.Subsequently,a deep neural network prediction model is developed for heavy distillate oil to predict its composition in terms of molecular structure.After training,the model accurately predicts the molecular composition of catalytically cracked raw oil in a refinery.The validation and test sets exhibit R2 values of 0.99769 and 0.99807,respectively,and the average relative error of molecular composition prediction for raw materials of the catalytic cracking unit is less than 7%.Finally,the SHAP(SHapley Additive ExPlanation)interpretation method is used to disclose the relationship among different variables by performing global and local weight comparisons and correlation analyses.

Double plasma molecular adsorption system for Stevens–Johnson syndrome/toxic epidermal necrolysis:A case report

BACKGROUND Stevens–Johnson syndrome and toxic epidermal necrolysis(SJS/TEN)are very serious skin allergies,with an etiology related to infections and medication.Since the coronavirus disease 2019(COVID-19)pandemic,severe acute respiratory syndrome coronavirus-2 has also been considered to cause SJS/TEN.CASE SUMMARY We report the case of a woman in her thirties who took acetaminophen after contracting COVID-19.After 3 d of fever relief,she experienced high fever and presented with SJS/TEN symptoms,accompanied by intrahepatic cholestasis.Three days of corticosteroid treatment did not alleviate the skin damage;therefore,double plasma molecular adsorption system(DPMAS)therapy was initiated,with treatment intervals of 48 h.Her skin symptoms improved gradually and were resolved after seven DPMAS treatments.CONCLUSION DPMAS therapy is beneficial for abrogating SJS/TEN because plasma adsorption and perfusion techniques reduce the inflammatory mediators(e.g.,tumor necrosis factor-alpha and interleukin-10 and-12)speculated to be involved in the pathology of the skin conditions.

The prognostic role of circulating tumor DNA across breast cancer molecular subtypes:A systematic review and meta-analysis

Objective:Circulating tumor DNA(ctDNA)is increasingly being used as a potential prognostic biomarker in cancer patients.We aimed to assess the prognostic value of ctDNA in different subtypes of breast cancer patients throughout the whole treatment cycle.Materials and methods:PubMed,Web of Science,Embase,Cochrane Library,Scopus,and clinical trials.gov databases were searched from January 2016 to May 2022.The following search terms were used:ctDNA OR circulating tumor DNA AND breast cancer OR breast carcinoma.Only studies written in English were included.The following pre-specified criteria should be met for inclusion:(i)original articles,conference abstracts,etc.;(ii)patients with breast cancer;(iii)ctDNA measurement;and(iv)clinical outcome data such as recurrence-free survival(RFS)and overall survival(OS).The random-effects model was preferred considering the potential het-erogeneity across studies.The main outcomes are ctDNA detection rate and postoperative long-term outcomes(RFS and OS).Results:A total of 24 studies were screened.At every measurement time,the ctDNA detection rate of the HR+subgroup was similar to that of the HR-subgroup(P=0.075;P=0.458;P=0.744;and P=0.578),and the ctDNA detection rate of the HER2+subgroup was similar to that of the HER2-subgroup(P=0.805;P=0.271;P=0.807;and P=0.703).In the HR+subgroup,RFS and OS of ctDNA positive patients were similar to those of ctDNA negative patients(P=0.589 and P=0.110),while RFS and OS of the ctDNA positive group was significantly shorter than those of the ctDNA negative patients in the HR-subgroup(HR=4.03,P<0.001;HR=3.21,P<0.001).According to HER grouping,the results were the same as above.In the triple negative breast cancer(TNBC)subgroup,the RFS and OS of ctDNA-positive patients was significantly shorter than of the ctDNA negative patients before and after surgery.Conclusions:ctDNA was more predictive of recurrence-free survival and overall survival in the HR-subgroup than in the HR+subgroup,and the same result was showed in the HER2-subgroup vs.HER2+subgroup.The prognosis of the TNBC subtype is closely related to ctDNA before and after surgery.

Molecular Structure Tailoring of Organic Spacers for High‑Performance Ruddlesden–Popper Perovskite Solar Cells

Layer-structured Ruddlesden–Popper(RP)perovskites(RPPs)with decent stability have captured the imagination of the photovoltaic research community and bring hope for boosting the development of perovskite solar cell(PSC)technology.However,two-dimensional(2D)or quasi-2D RP PSCs are encountered with some challenges of the large exciton binding energy,blocked charge transport and poor film quality,which restrict their photovoltaic performance.Fortunately,these issues can be readily resolved by rationally designing spacer cations of RPPs.This review mainly focuses on how to design the molecular structures of organic spacers and aims to endow RPPs with outstanding photovoltaic applications.We firstly elucidated the important roles of organic spacers in impacting crystallization kinetics,charge transporting ability and stability of RPPs.Then we brought three aspects to attention for designing organic spacers.Finally,we presented the specific molecular structure design strategies for organic spacers of RPPs aiming to improve photovoltaic performance of RP PSCs.These proposed strategies in this review will provide new avenues to develop novel organic spacers for RPPs and advance the development of RPP photovoltaic technology for future applications.

Decoding molecular mechanisms:brain aging and Alzheimer's disease

The complex morphological,anatomical,physiological,and chemical mechanisms within the aging brain have been the hot topic of research for centuries.The aging process alters the brain structure that affects functions and cognitions,but the worsening of such processes contributes to the pathogenesis of neurodegenerative disorders,such as Alzheimer's disease.Beyond these observable,mild morphological shifts,significant functional modifications in neurotransmission and neuronal activity critically influence the aging brain.Understanding these changes is important for maintaining cognitive health,especially given the increasing prevalence of age-related conditions that affect cognition.This review aims to explore the age-induced changes in brain plasticity and molecular processes,differentiating normal aging from the pathogenesis of Alzheimer's disease,thereby providing insights into predicting the risk of dementia,particularly Alzheimer's disease.

High mobility group box 1 in the central nervous system:regeneration hidden beneath inflammation

High-mobility group box 1 was first discovered in the calf thymus as a DNA-binding nuclear protein and has been widely studied in diverse fields,including neurology and neuroscience.High-mobility group box 1 in the extracellular space functions as a pro-inflammatory damage-associated molecular pattern,which has been proven to play an important role in a wide variety of central nervous system disorders such as ischemic stroke,Alzheimer’s disease,frontotemporal dementia,Parkinson’s disease,multiple sclerosis,epilepsy,and traumatic brain injury.Several drugs that inhibit high-mobility group box 1 as a damage-associated molecular pattern,such as glycyrrhizin,ethyl pyruvate,and neutralizing anti-high-mobility group box 1 antibodies,are commonly used to target high-mobility group box 1 activity in central nervous system disorders.Although it is commonly known for its detrimental inflammatory effect,high-mobility group box 1 has also been shown to have beneficial pro-regenerative roles in central nervous system disorders.In this narrative review,we provide a brief summary of the history of high-mobility group box 1 research and its characterization as a damage-associated molecular pattern,its downstream receptors,and intracellular signaling pathways,how high-mobility group box 1 exerts the repair-favoring roles in general and in the central nervous system,and clues on how to differentiate the pro-regenerative from the pro-inflammatory role.Research targeting high-mobility group box 1 in the central nervous system may benefit from differentiating between the two functions rather than overall suppression of high-mobility group box 1.

Molecular simulation study of the microstructures and properties of pyridinium ionic liquid[HPy][BF_(4)]mixed with acetonitrile

The microstructures and thermodynamic properties of mixed systems comprising pyridinium ionic liquid[HPy][BF_(4)]and acetonitrile at different mole fractions were studied using molecular dynamics simulation in this work.The following properties were determined:density,self-diffusion coefficient,excess molar volume,and radial distribution function.The results show that with an increase in the mole fraction of[HPy][BF_(4)],the self-diffusion coefficient decreases.Additionally,the excess molar volume initially decreases,reaches a minimum,and then increases.The rules of radial distribution functions(RDFs)of characteristic atoms are different.With increasing the mole fraction of[HPy][BF_(4)],the first peak of the RDFs of HA1-F decreases,while that of CT6-CT6 rises at first and then decreases.This indicates that the solvent molecules affect the polar and non-polar regions of[HPy][BF_(4)]differently.

MODELING AND NUMERICAL SIMULATION OF ONBOARD MOLECULAR SIEVE OXYGEN GENERATION SYSTEM

A mathematical model for simulating concentric-bed and other components of molecular sieve oxygen concentrator is established. In the model, the binary Langmuir equilibrium adsorption equation is adopted to describe the adsorption performance of the adsorbent, the linear driving force (LDF) model is used to describe the mass transfer rate, and the thermal effect during adsorption is considered. The finite difference method is used in simulation and comparison. Numerical results have a reasonable agreement with the experimental research.

Semiconductor,molecular and hybrid systems for photoelectrochemical solar fuel production

The paper shortly reviews the basic direct approaches applied in searching for viable solutions to solar fuel production. These are generally distinguished in molecular and semiconductor(non-molecular)systems, however, hybrid strategies, proposed recently, have also been included. The most promising efforts are considered, highlighting key aspects and emerging critical issues. Special attention is paid to aspects such as electrode architecture, device design, and main differences in the scientific vision and challenges to directly produce solar fuels. This overview could be useful to orientate the readers in the wide panorama of research activities concerning water splitting, natural and artificial photosynthesis, and solar fuel production through the identification of common aspects, specialties and potentialities of the many initiatives and approaches that are developing worldwide in this field with the final aim to meet world energy demand.

Studies on Molecular Mechanism of Human Early Cardiogenesis Using the Drosophila as a Model System

Recently,some of the genetic mechanisms of heart specification have been elucidated in Drosophila .However,genes involved in early cardiogenesis of human remain to be identified.Since the pathways that regulate early cardiac fate determination are conserved between Drosophila and vertebrates,flies can be used as a model test system to explore the genetic basis of cardiogenesis in human.In this project,about 3000 reccieve lethal gene lines were produced by P or EMS mutagenesis.With staining of antibodies against heart precussor cells of Drosophila ,about 200 lines were observed to show heart phenotype.In pilot studies of their function with RNAi technique,the RNAi phenotypes of several genes tested were observed,which were very similar to that of their mutants,showing heart tube defects or no heart precursors formation.Taking advantage of the advanced genetic information available in the Drosophila and human systems,we have identified about 50 human transcripts homologous to the Drosophila heart related gene candidates.Northern blot analysis for some of the human candidates showed that several genes were expressed in both adult and early embryonic tissues,which may help in the evaluation of candidate genes for human cardiogenesis.Our further experiments with transgenic flies generated with wild type and mutant forms of these candidate genes to examine for defects in cardiogenesis or cardiac function are under way.The candidate genes producing cardiac specific defects suggestive of similarities to the heart disease syndromes can then be pursued further as likely disease gene candidates.Such an approach is likely to provide a dramatic reduction of possible candidate genes,or to screen and identify mutations that may generate the disease in human.

Hyperspherical Harmonic Expansions of Potential 1/r_(jt) of Molecular Systems

The expansion coefficient C D |L| of Coulomb potential 1/r jt of molecular systems in hyperspherical harmonics is derived in detail, and the explicit expression is given.

Molecular systematics analysis of Lymantria dispar based on 18S rRNA and cox1 mtDNA sequence data

The complete sequence of the 18S ribosomal RNA gene （18S rRNA） from Lymantria dispar was cloned and analysed here. 18S rRNA and mitochondrial cytochrome c oxidasel （coxl） gene sequences of Lymantria dispar were compared with homologous sequences of other nine insects from different orders. Analytic results showed that 18S rRNA of these insects had two conserved domains and the second domain was an even more conserved region. The phylogenetic trees based on the full-length sequence and the second domain fragment of 18S rRNA as well as sequence of coxl from different orders indicated that Lepidoptera and Trichoptera, which belongs to Amphiesmenoptera, had a closer phylogenetic relationship and fewer differences were observed comparing with traditional taxonomic results.

Irinotecan therapy and molecular targets in colorectal cancer: A systemic review

Irinotecan is the second line chemotherapy for advanced stage colorectal cancer (CRC) after failure of first line chemotherapy with oxaliplatin and 5-fluorouracil. The aim of this review is to analyse the data on irinotecan as second line chemotherapy for advanced CRC and the potential roles of the molecular markers, p53 and vascular endothelial growth factor (VEGF) in the management of advanced CRC. Thus, the English literature from 1980 to 2008 concerning irinotecan, p53, VEGF and CRC was reviewed. On review, Phase and clinical trials showed thatirinotecan improves pain-free survival, quality of life, 1-year survival, progression-free survival and overall survival in advanced CRC. p53 and VEGF were expressed in CRC and had a predictive power of aggressive clinical behaviour in CRC. Irinotecan sensitizes p53 wild type, mutant and null cells to Fasmediated cell apoptosis in CRC cells. Wild type p53 cells were more sensitive to irinotecan than mutated p53. Irinotecan has an anti-VEGF effect inhibiting endothelial cell proliferation, increasing apoptosis and reducing microvascular density which is onlylimited by irinotecan toxicity levels. To conclude, irinotecan improves the patient's quality of life and the survival rates of patients with advanced CRC. p53 and VEGF status of the patients' tumour is likely to affect the responsiveness of CRC to irinotecan. It is recommended that studies of the expression of these molecular markers in relation to chemoresponsiveness ofirinotecan should be carried out for better management of patients with advanced CRC.

Molecular adsorbent recycling system in treat-ing patients with acute liver failure: a bridge to liver transplantation

BACKGROUND:Acute liver failure is still a life-threaten- ing disease although it can be treated by liver transplanta- tion. This study was conducted to assess the molecular ad- sorbent recycling system (MARS), which may bridge acute liver failure patients to liver transplantation. METHODS: Biochemical indexes and other clinical data were analyzed of 8 patients with acute liver failure, who had been treated by MARS for 34 times and subsequent Piggyback liver transplantation. RESULTS: After treatment with MARS, the levels of tran- saminase and total bilirubin decreased markedly, but coagu- lation function remained unimproved. All patients survived and discharged from the hospital. CONCLUSION: MARS is effective in bridging patients with acute liver failure to liver transplantation.