Computational Molecular Biology(ISSN 1927-5587)is an open access,peer reviewed journal published online by Bio Publisher.The Journal is publishing all the latest and outstanding research articles,letters,methods,and r...Computational Molecular Biology(ISSN 1927-5587)is an open access,peer reviewed journal published online by Bio Publisher.The Journal is publishing all the latest and outstanding research articles,letters,methods,and reviews in all areas of Computational Molecular Biology,covering new discoveries in molecular biology,from genes展开更多
Computational Molecular Biology(ISSN 1927-5587)is an open access,peer reviewed journal published online by Bio Publisher.The Journal is publishing all the latest and outstanding research articles,letters,methods,and r...Computational Molecular Biology(ISSN 1927-5587)is an open access,peer reviewed journal published online by Bio Publisher.The Journal is publishing all the latest and outstanding research articles,letters,methods,and reviews in all areas of Computational Molecular Biology,covering new discoveries in molecular biology,from genes展开更多
Computational Molecular Biology(ISSN 1927-5587)is an open access,peer reviewed journal published online by Bio Publisher.The Journal is publishing all the latest and outstanding research articles,letters,methods,and r...Computational Molecular Biology(ISSN 1927-5587)is an open access,peer reviewed journal published online by Bio Publisher.The Journal is publishing all the latest and outstanding research articles,letters,methods,and reviews in all areas of Computational Molecular Biology,covering new discoveries in molecular biology,展开更多
Computational Molecular Biology(ISSN 1927-5587)is an open access,peer reviewed journal published online by Bio Publisher.The Journal is publishing all the latest and outstanding research articles,letters,methods,and r...Computational Molecular Biology(ISSN 1927-5587)is an open access,peer reviewed journal published online by Bio Publisher.The Journal is publishing all the latest and outstanding research articles,letters,methods,and reviews in all areas of Computational Molecular Biology,covering new discoveries in molecular biology,from genes to genomes,using statistical,mathematical,and computational methods as well as展开更多
Stimuli-responsive DNA-based logic gates have emerged as a promising field at the intersection of synthetic biology and nanotechnology.These gates exploit the unique properties of DNA molecules to perform programmable...Stimuli-responsive DNA-based logic gates have emerged as a promising field at the intersection of synthetic biology and nanotechnology.These gates exploit the unique properties of DNA molecules to perform programmable computational operations in response to specific stimuli.This review provides a comprehensive overview of recent advancements in the design,working principles,and applications of stimuli-responsive DNA-based logic gates.The progress made in developing various types of logic gates triggered by metal ions,pH,oligonucleotides,small molecules,proteins,and light is highlighted.The applications of these logic gates in imaging and biosensing,drug delivery,synthetic biology and molecular computing are discussed.This review underscores the significant contributions and future prospects of stimuli-responsive DNA-based logic gates in advancing the field of nanotechnology.展开更多
The generation of various entangled states is an essential task in quantum information processing. Recently, a scheme （PRA 79, 022304） has been suggested for generating Greenberger-Horne-Zeilinger state and cluster ...The generation of various entangled states is an essential task in quantum information processing. Recently, a scheme （PRA 79, 022304） has been suggested for generating Greenberger-Horne-Zeilinger state and cluster state with atomic ensembles based on the Rydberg blockade. Using similar resources as the earlier scheme, here we propose an experimentally feasible scheme of preparing arbitrary four-qubit W class of maximally and non- maximally entangled states with atomic ensembles in a single step. Moreover, we carefully analyze the realistic noises and predict that four-qubit W states can be produced with high fidelity （F - 0.994） via our scheme.展开更多
A protocol is proposed to implement a three-qubit phase gate for photonic qubits in a three-mode cavity. The idea can be extended to directly implement a N-qubit phase gate. We also show that the interaction time rema...A protocol is proposed to implement a three-qubit phase gate for photonic qubits in a three-mode cavity. The idea can be extended to directly implement a N-qubit phase gate. We also show that the interaction time remains unchanged with the increasing number of qubits. In addition, the influence of cavity decay and atomic spontaneous emission on the gate fidelity and photon loss probability is also discussed by numerical calculation.展开更多
One-dimensional deposition of a neutral chromium atomic beam focused by a near-resonant Gaussian standing- laser field is discussed by using a fourth-order Runge-Kutta type algorithm. The deposition pattern of neutral...One-dimensional deposition of a neutral chromium atomic beam focused by a near-resonant Gaussian standing- laser field is discussed by using a fourth-order Runge-Kutta type algorithm. The deposition pattern of neutral chromium atoms in a laser standing wave with different laser power is discussed and the simulation result shows that the full width at half maximum （FWHM） of a nanometer stripe is 115nm and the contrast is 2.5：1 with laser power 3.93mW; the FWHM is 0.8nm and the contrast is 27：1 with laser power 16mW, the optimal laser power; but with laser power increasing to 50mW, the nanometer structure forms multi-crests and the quality worsens quickly with increasing laser power.展开更多
We investigate the energy spectrum of ultracold atoms on the two-dimensional Kagomé optical lattice under an effective magnetic field, which can be realized with laser beams. We derive the generalized Harper＇s e...We investigate the energy spectrum of ultracold atoms on the two-dimensional Kagomé optical lattice under an effective magnetic field, which can be realized with laser beams. We derive the generalized Harper＇s equations from the Schr？dinger equation. The energy spectrum with a fractal band structure is obtained by numerically solving the generalized Harper＇s equations. We analyze the properties of the Hofstadter＇s butterfly spectrum and discuss its observability.展开更多
BACKGROUND Regulatory T cells(Tregs)and natural killer(NK)cells play an essential role in the development of bladder urothelial carcinoma(BUC).AIM To construct a prognosis-related model to judge the prognosis of patie...BACKGROUND Regulatory T cells(Tregs)and natural killer(NK)cells play an essential role in the development of bladder urothelial carcinoma(BUC).AIM To construct a prognosis-related model to judge the prognosis of patients with bladder cancer,meanwhile,predict the sensitivity of patients to chemotherapy and immunotherapy.METHODS Bladder cancer information data was obtained from The Cancer Genome Atlas and GSE32894.The CIBERSORT was used to calculate the immune score of each sample.Weighted gene co-expression network analysis was used to find genes that will have the same or similar expression patterns.Subsequently,multivariate cox regression and lasso regression was used to further screen prognosis-related genes.The prrophetic package was used to predict phenotype from gene expression data,drug sensitivity of external cell line and predict clinical data.RESULTS The stage and risk scores are independent prognostic factors in patients with BUC.Mutations in FGFR3 lead to an increase in Tregs percolation and affect the prognosis of the tumor,and additionally,EMP1,TCHH and CNTNAP3B in the model are mainly positively correlated with the expression of immune checkpoints,while CMTM8,SORT1 and IQSEC1 are negatively correlated with immune checkpoints and the high-risk group had higher sensitivity to chemotherapy drugs.CONCLUSION Prognosis-related models of bladder tumor patients,based on Treg and NK cell percolation in tumor tissue.In addition to judging the prognosis of patients with bladder cancer,it can also predict the sensitivity of patients to chemotherapy and immunotherapy.At the same time,patients were divided into high and low risk groups based on this model,and differences in genetic mutations were found between the high and low risk groups.展开更多
The differential and integral cross sections for electron impact excitation of lithium from the ground state 1s22s to excited states 1s22p, 1s23l （l=s, p, d） and 1s24l （l=s, p, d, f）at incident energies ranging fr...The differential and integral cross sections for electron impact excitation of lithium from the ground state 1s22s to excited states 1s22p, 1s23l （l=s, p, d） and 1s24l （l=s, p, d, f）at incident energies ranging from 5 eV to 25 eV are calculated by using a full relativistic distorted wave method. The target state wavefunctions are calculated by using the Grasp92 code. The continuum orbitals are computed in the distorted-wave approximation, in which the direct and exchange potentials among all the electrons are included. A part of the cross sections are compared with the available experimental data and with the previous theoretical values. It is found that, for the integral cross sections, the present calculations are in good agreement with the time-independent distorted wave method calculation, for differential cross sections, our results agree with the experimental data very well.展开更多
A cloud of laser-cooled ^40Ca^＋ is successfully trapped and manipulated under well control in our home-built linear ion trap, which is designed and constructed solely for studying quantum information processing. By e...A cloud of laser-cooled ^40Ca^＋ is successfully trapped and manipulated under well control in our home-built linear ion trap, which is designed and constructed solely for studying quantum information processing. By exploring the variation of the ion cloud with respect to the trap parameters, we have optimized the trapping condition and obtained very good fluorescence spectra. We observe the dynamics of the ion cloud, and estimate the temperature of the ion cloud to be of the order of milli-Kelvin.展开更多
Molecular information gathering and proces- sing -- a young field of applied chemistry -- is undergoing good growth. The progress is occurring both in terms of conceptual development and in terms of the strengthening ...Molecular information gathering and proces- sing -- a young field of applied chemistry -- is undergoing good growth. The progress is occurring both in terms of conceptual development and in terms of the strengthening of older concepts with new examples. This review critically surveys these two broad avenues. We consider some cases where molecules emulate one of the building blocks of electronic logic gates. We then examine molecular emulation of various Boolean logic gates carrying one, two or three inputs. Some single-input gates are popular information gathering devices. Special systems, such as ＇lab-on-a-molecule＇ and molecular key- pad locks, also receive attention. A situation deviating from the Boolean blueprint is also discussed. Some pointers are offered for maintaining the upward curve of the field.展开更多
文摘Computational Molecular Biology(ISSN 1927-5587)is an open access,peer reviewed journal published online by Bio Publisher.The Journal is publishing all the latest and outstanding research articles,letters,methods,and reviews in all areas of Computational Molecular Biology,covering new discoveries in molecular biology,from genes
文摘Computational Molecular Biology(ISSN 1927-5587)is an open access,peer reviewed journal published online by Bio Publisher.The Journal is publishing all the latest and outstanding research articles,letters,methods,and reviews in all areas of Computational Molecular Biology,covering new discoveries in molecular biology,from genes
文摘Computational Molecular Biology(ISSN 1927-5587)is an open access,peer reviewed journal published online by Bio Publisher.The Journal is publishing all the latest and outstanding research articles,letters,methods,and reviews in all areas of Computational Molecular Biology,covering new discoveries in molecular biology,
文摘Computational Molecular Biology(ISSN 1927-5587)is an open access,peer reviewed journal published online by Bio Publisher.The Journal is publishing all the latest and outstanding research articles,letters,methods,and reviews in all areas of Computational Molecular Biology,covering new discoveries in molecular biology,from genes to genomes,using statistical,mathematical,and computational methods as well as
基金supported by Hong Kong Research Grants Council(11307421,11301220,and 11304719)Health and Medical Research Fund(09203576 and 07181396)+2 种基金National Science Foundation of China(21574109 and 217780430)The Science and Technology Innovation Committee of Shenzhen Municipality(JCYJ20190812160203619)City University of Hong Kong 7005832 and 7006006.
文摘Stimuli-responsive DNA-based logic gates have emerged as a promising field at the intersection of synthetic biology and nanotechnology.These gates exploit the unique properties of DNA molecules to perform programmable computational operations in response to specific stimuli.This review provides a comprehensive overview of recent advancements in the design,working principles,and applications of stimuli-responsive DNA-based logic gates.The progress made in developing various types of logic gates triggered by metal ions,pH,oligonucleotides,small molecules,proteins,and light is highlighted.The applications of these logic gates in imaging and biosensing,drug delivery,synthetic biology and molecular computing are discussed.This review underscores the significant contributions and future prospects of stimuli-responsive DNA-based logic gates in advancing the field of nanotechnology.
基金Supported by the National Natural Science Foundation of China under Grant No 10774192, the Fund of Innovation of Graduate School of National University of Defense Technology under Grant No 080201.
文摘The generation of various entangled states is an essential task in quantum information processing. Recently, a scheme （PRA 79, 022304） has been suggested for generating Greenberger-Horne-Zeilinger state and cluster state with atomic ensembles based on the Rydberg blockade. Using similar resources as the earlier scheme, here we propose an experimentally feasible scheme of preparing arbitrary four-qubit W class of maximally and non- maximally entangled states with atomic ensembles in a single step. Moreover, we carefully analyze the realistic noises and predict that four-qubit W states can be produced with high fidelity （F - 0.994） via our scheme.
文摘A protocol is proposed to implement a three-qubit phase gate for photonic qubits in a three-mode cavity. The idea can be extended to directly implement a N-qubit phase gate. We also show that the interaction time remains unchanged with the increasing number of qubits. In addition, the influence of cavity decay and atomic spontaneous emission on the gate fidelity and photon loss probability is also discussed by numerical calculation.
文摘One-dimensional deposition of a neutral chromium atomic beam focused by a near-resonant Gaussian standing- laser field is discussed by using a fourth-order Runge-Kutta type algorithm. The deposition pattern of neutral chromium atoms in a laser standing wave with different laser power is discussed and the simulation result shows that the full width at half maximum （FWHM） of a nanometer stripe is 115nm and the contrast is 2.5：1 with laser power 3.93mW; the FWHM is 0.8nm and the contrast is 27：1 with laser power 16mW, the optimal laser power; but with laser power increasing to 50mW, the nanometer structure forms multi-crests and the quality worsens quickly with increasing laser power.
文摘We investigate the energy spectrum of ultracold atoms on the two-dimensional Kagomé optical lattice under an effective magnetic field, which can be realized with laser beams. We derive the generalized Harper＇s equations from the Schr？dinger equation. The energy spectrum with a fractal band structure is obtained by numerically solving the generalized Harper＇s equations. We analyze the properties of the Hofstadter＇s butterfly spectrum and discuss its observability.
文摘BACKGROUND Regulatory T cells(Tregs)and natural killer(NK)cells play an essential role in the development of bladder urothelial carcinoma(BUC).AIM To construct a prognosis-related model to judge the prognosis of patients with bladder cancer,meanwhile,predict the sensitivity of patients to chemotherapy and immunotherapy.METHODS Bladder cancer information data was obtained from The Cancer Genome Atlas and GSE32894.The CIBERSORT was used to calculate the immune score of each sample.Weighted gene co-expression network analysis was used to find genes that will have the same or similar expression patterns.Subsequently,multivariate cox regression and lasso regression was used to further screen prognosis-related genes.The prrophetic package was used to predict phenotype from gene expression data,drug sensitivity of external cell line and predict clinical data.RESULTS The stage and risk scores are independent prognostic factors in patients with BUC.Mutations in FGFR3 lead to an increase in Tregs percolation and affect the prognosis of the tumor,and additionally,EMP1,TCHH and CNTNAP3B in the model are mainly positively correlated with the expression of immune checkpoints,while CMTM8,SORT1 and IQSEC1 are negatively correlated with immune checkpoints and the high-risk group had higher sensitivity to chemotherapy drugs.CONCLUSION Prognosis-related models of bladder tumor patients,based on Treg and NK cell percolation in tumor tissue.In addition to judging the prognosis of patients with bladder cancer,it can also predict the sensitivity of patients to chemotherapy and immunotherapy.At the same time,patients were divided into high and low risk groups based on this model,and differences in genetic mutations were found between the high and low risk groups.
文摘The differential and integral cross sections for electron impact excitation of lithium from the ground state 1s22s to excited states 1s22p, 1s23l （l=s, p, d） and 1s24l （l=s, p, d, f）at incident energies ranging from 5 eV to 25 eV are calculated by using a full relativistic distorted wave method. The target state wavefunctions are calculated by using the Grasp92 code. The continuum orbitals are computed in the distorted-wave approximation, in which the direct and exchange potentials among all the electrons are included. A part of the cross sections are compared with the available experimental data and with the previous theoretical values. It is found that, for the integral cross sections, the present calculations are in good agreement with the time-independent distorted wave method calculation, for differential cross sections, our results agree with the experimental data very well.
基金Supported by the National Natural Science Foundation of China under the Grant Nos 10774163, 10774161 and 10974225, and the National Fundamental Research Program of China under Grant No 2006CB921203. We acknowledge thankfully Professor C. Wunderlich, and Professor D. Suter for help and/or discussion, and we are grateful to Professor Zhan Mingsheng and Professor Gao Kelin for support and encouragement.
文摘A cloud of laser-cooled ^40Ca^＋ is successfully trapped and manipulated under well control in our home-built linear ion trap, which is designed and constructed solely for studying quantum information processing. By exploring the variation of the ion cloud with respect to the trap parameters, we have optimized the trapping condition and obtained very good fluorescence spectra. We observe the dynamics of the ion cloud, and estimate the temperature of the ion cloud to be of the order of milli-Kelvin.
文摘Molecular information gathering and proces- sing -- a young field of applied chemistry -- is undergoing good growth. The progress is occurring both in terms of conceptual development and in terms of the strengthening of older concepts with new examples. This review critically surveys these two broad avenues. We consider some cases where molecules emulate one of the building blocks of electronic logic gates. We then examine molecular emulation of various Boolean logic gates carrying one, two or three inputs. Some single-input gates are popular information gathering devices. Special systems, such as ＇lab-on-a-molecule＇ and molecular key- pad locks, also receive attention. A situation deviating from the Boolean blueprint is also discussed. Some pointers are offered for maintaining the upward curve of the field.
