Tag: SCF

Ab Initio Molecular Dynamics CP2K is a program to perform simulations of solid state, liquid, molecular and biological systems. It is especially aimed at massively parallel and linear scaling electronic structure methods and state-of-the-art ab-initio molecular dynamics (AIMD) simulations. CP2K is optimized for the mixed Gaussian and Plane-Waves (GPW) method…

Can sangeranalyseR be changed to read SCF files? 0 Hello! I am working with sanger sequences where half of them are in the ab1/abi format, the other half is scf. I am using sangeranalyseR, an R package (github.com/roblanf/sangeranalyseR), to do quality-trimming and alignment of my ab1 files, and all seemed…

Natural killer (NK) cells are innate lymphocytes that play a key role in the control of infection and malignancy. NK cells are potent killers of target cells and act in an MHC-independent manner, enabling their application as allogenic therapy for cancer. Human iPSCs are pluripotent with the ability to self-renew,…

All All Products Enzymes Receptors Ion Channels Research Areas Oxidoreductases Transferases Lyases Isomerases Ligases Nuclear Receptors Ligand-gated ATP-Sensitive Angiogenesis Apoptosis Cardiovascular Cell Cycle Regulation Cell Signaling & Oncology CNS Diabetes & Metabolism Epigenetics Immunology Miscellaneous Pain & Inflammation Stem Cell Oxidases MAO Cys-loop, cationic Cis-Trans Isomerase CypA DNA Topoisomerase Synthetases…

Cellular immunotherapy—for example, Chimeric Antigen Receptor (CAR)-T cell therapy—has shown great efficacy in treating various hematologic malignancies. CAR-T therapy has undergone notable changes, and several drugs have received regulatory approval for commercial use. Despite these achievements, substantial challenges remain in the widespread use of autologous CAR-T therapy, such as the…

Dear developers and users: I wish to ask what to do,  if using a restart file from a previous metadynamic run  (updated to inp extension: please, see the attached) CP2K terminates with a notice Cholesky decompose failed: the matrix is not positive definite or * *    |      …

ddiaz (Daniel Diaz) December 1, 2023, 10:07pm 1 I was hoping to get advice on implementing a loss function in a surrogate model. I am working with micromechanical simulations of gas pores produced during processing in Additive Manufacturing, and due to the simulation time I put together a surrogate model…

What is a endoglycosidase H?3 answersEndoglycosidase H (Endo H) is a glycosidase enzyme that cleaves N-linked glycans from glycoproteins. It is commonly used in research to analyze protein glycosylation and to study glycoprotein trafficking. Endo H specifically cleaves high mannose and some hybrid N-glycans, but not complex N-glycans. It is…

. 2023 Nov 26;80(12):374. doi: 10.1007/s00018-023-05019-9. Affiliations Expand Affiliations 1 School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, 695551, India. 2 School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, 695551, India. tmanna@iisertvm.ac.in. Item in Clipboard Vishnu M Nair et…

Dear CP2K users   I try to calculate core binding energies using GW calculations. I am interested in the Cl2p line of a Cl- ion on the top of Mg*6H2O crystal:  I performed a first-principle MD, and due to the computational/ memory cost of the calculations, I extracted different snapshots…

Ethical considerations This study complies with relevant institutional, national, and international guidelines and legislation. The Ethics Committee at the RIKEN Center for Integrative Medical Sciences (H30-4) approved this study, and written informed consent was obtained from all volunteers who provided specimens. Sampling solutions The AgST solution was prepared as follows:…

Abstract The importance of glial cells, mainly astrocytes, oligodendrocytes, and microglia, in the central nervous system (CNS) has been increasingly appreciated. Recent advances have demonstrated the diversity of glial cells and their contribution to human CNS development, normal CNS functions, and disease progression. The uniqueness of human glial cells is…

I want to calculate the IR spectra of a organic molecule adsorbed on a Au(111) slab. I optimized the structure with a tight SCF convergence and tight force threshold. The problem occurs when I run the VIBRATIONAL_ANALYSIS calculation (using &PROPERTIES&LINRES&POLAR PERIODIC_DIPOLE_OPERATOR TRUE) and I can read at the end of the…

doi: 10.1002/1878-0261.13537. Online ahead of print. Joseph S Baxter  1   2 , Rachel Brough  1   2 , Dragomir B Krastev  1   2 , Feifei Song  1   2 , Sandhya Sridhar  1   2 , Aditi Gulati  2 , John Alexander  2 , Theodoros I Roumeliotis  3 , Zuza Kozik  3 , Jyoti S Choudhary  3…

Ding, L., Saunders, T. L., Enikolopov, G. & Morrison, S. J. Endothelial and perivascular cells maintain haematopoietic stem cells. Nature 481, 457–462 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Ding, L. & Morrison, S. J. Haematopoietic stem cells and early lymphoid progenitors occupy distinct bone marrow niches. Nature 495,…

Culture of human-induced pluripotent stem cells (hiPSCs) Human iPSC lines were cultured in Matrigel-coated plates in the Nutristem medium (Corning, USA). Cells were passaged every 5 days by treating with Versene (Thermo Fisher Scientific, USA) for 3–5 min, transferred to freshly prepared Matrigel-coated plates, and cultured under hypoxic conditions with 5% CO2…

Architecture independent files for Staden Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin). Gap4 performs sequence assembly, contig ordering based on read pair data, contig joining based on sequence comparisons, assembly checking, repeat searching, experiment suggestion, read pair analysis and…

Dear CP2K team, I am attempting to calculate the single point energy of a huge periodic cluster (near 5k atoms, just contains C H O N, cell size 30+ angstrom, only Gamma point). Due to the demand of following analysis, I used B3LYP hybrid functional (with D3(BJ)) and 6-31G(d)…

HDFC Bank Phase3 B2 Mohali IFSC Code is HDFC0001209. The Phase3 B2 Mohali IFSC Code could be used for electronic fund transfer like NEFT, RTGS etc. In this IFSC Code HDFC0001209, 001209 is assign to the HDFC Bank Phase3 B2 Mohali branch and first four characters (HDFC) are identical for…

Hi Daniele, I once wrote a parser for the molecular orbital coefficients in Python: github.com/ondrejkrejci/PPSTM/blob/master/pyPPSTM/ReadSTM.py#L520 You can obtain the MO file like this: &DFT &PRINT &MO ON EIGVECS CARTESIAN FILENAME cartesian-mos &EACH QS_SCF 0 &END EACH &END MO &END PRINT &END DFT -Ole On 2018-09-27 10:09, Daniele Ongari wrote: > Thank you for the hint, but I think something is going weir…

Dear CP2K Community, I am currently attempting to use a .molden file as the Restart file for SCF_GUESS in CP2K, but I have encountered a “nspin is not equal” warning and a subsequent “Reducing nspin is not possible” error. To provide additional context, I have attached both the input and…

FBXW7 is a critical regulator of cell cycle, cell signaling, and development. A highly conserved F-box protein and component of the SKP1-Cullin-F-box (SCF) complex, FBXW7 functions as a recognition subunit within a Cullin-RING E3 ubiquitin ligase responsible for ubiquitinating substrate proteins and targeting them for proteasome-mediated degradation. In human cells,…

From yeast to humans, FBXW7 proteins share three conserved domains: a dimerization domain required for interaction of two FBXW7 protomers, an F-box domain that mediates FBXW7 interaction with SKP1, and a substrate-binding domain composed of eight WD40 repeats (Figure 1A). The human FBXW7 gene permits expression of three isoforms that…

Overexpression of Rhox6 promotes PGCLC formation To discover potential candidate genes that may be important for the specification of mouse PGCs, we analyzed the transcriptional data of E9.5 PGCs and epiblasts and found that the homeobox family members Rhox6 and Rhox9, as well as the PGC markers Prdm14, Blimp1, Stella…

Peng, J. et al. ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature 400, 256–261 (1999). Article  CAS  PubMed  Google Scholar  Eshed, Y. & Lippman, Z. B. Revolutions in agriculture chart a course for targeted breeding of old and new crops. Science 366, eaax0025 (2019). Article  CAS  PubMed  Google Scholar …

Weinberg, R. A. The action of oncogenes in the cytoplasm and nucleus. Science 230, 770–776 (1985). Article  ADS  CAS  PubMed  Google Scholar  Davoli, T. et al. Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. Cell 155, 948–962 (2013). Article  CAS  PubMed  PubMed Central  Google Scholar  Sanchez-Vega,…

The F-Box and WD Repeat Domain Containing 7 (FBXW7) protein has been shown to regulate cellular growth and act as a tumor suppressor. This protein, also known as FBW7, hCDC4, SEL10 or hAGO, is encoded by the gene FBXW7. It is a crucial component of the Skp1-Cullin1-F-box (SCF) complex, which…

Dear CP2K users, I am currently working with a series of transition metal oxides and CP2K is working fine but when I try to converge a calculation on the mixed valence Cu oxide (Cu3O4) my calculations are not converging. I have read that this oxide is a tricky system for…

I tried to run the example file online by the command “cp2k.ssmp -o water.out water.inp &’, but the calculations aborted with the following error. Need your help. … …   SCF WAVEFUNCTION OPTIMIZATION   Step     Update method      Time    Convergence         Total energy    Change  …

Dear CP2K users   I would like to calculate core electron binding energy using GW100 method in CP2K. www.cp2k.org/howto:gw   I started with a simple test, using a sulfate ion, SO42-, in vacuum to calculate the S2p lines. I first optimized the structure of SO42- in vacuum at PBE level,…

I am attempting to run OPES Metadynamics in CP2K, using PLUMED as an external driver. I am encountering two problems with my setup: =================================== plumed_inupt_file UNITS LENGTH=A ENERGY=kcal/mol TIME=fscv1: DISTANCE ATOMS=4,13cv2: DISTANCE ATOMS=1,16opes: OPES_METAD_EXPLORE ARG=cv1,cv2 PACE=20 BARRIER=50 TEMP=300uwall: UPPER_WALLS ARG=cv1,cv2 AT=3.0,3.0 KAPPA=40,40PRINT STRIDE=20 FILE=COLVAR ARG=* ======================================= When I omit the…

I am trying to calculate molecular polarizability of a single CH4 molecular via cp2k software using the B3LYP functional and the d-aug-cc-pVDZ basis set. The strategy is as follows. By changing the polarization direction of the electric field, the corresponding molecular dipole moment is obtained, and then the molecular polarizability…

Dear CP2K users, I am kind of new using cp2k but I have been using the software fo a couple of months. I am trying to optimize both geometry and cell parameters of different semiconductor material but the obtained geometries are distorted compared with experimental data or relaxed geometries obtained…

Dear all, I am facing an issue while running AIMD simulations of a box of ~1000 atoms. The system is an amorphous MOF made of Fe linked by benzene tricarboxylate (named Fe-BTC). I use PBE functional with DZVP basis set and GTH pseudopotential ; DIIS method and…

Dear all, I have been trying to optimize a unit cell of the 2D semiconductor CrSBr using GPW method implemented in CP2K. The initial cell parameters were a = 3.6 A, b = 4.8 A and c = 25.0 A (obtained from previous calculations with Quantum Espresso and in good…

Annotation of short-read scRNA-seq data with isoform-level information Using fluorescence-activated cell sorting (FACS), we isolated the Lineage-negative, cKit (Cd117) positive (LK) cell fraction of mouse bone marrow cells, a population containing stem and progenitor cells14 from young (8 weeks old, n = 3) and aged (72+ weeks old, n = 3) mice. We generated…

Newswise — A gene regulating the F-Box and WD Repeat Domain Containing 7 (FBXW7) protein is frequently mutated or deleted in various types of human cancer, including gynecological cancers. Such FBXW7 mutations have been associated with poor prognosis due to increased resistance to treatment. Hence, detection of the FBXW7 mutation…

Cells and cell culture KOPN30, BV173, and K562 are BCR/ABL1-positive leukemia cell lines. All leukemia cell lines, as well as Ba/F3 cells, were maintained in RPMI-1640 medium supplemented with 15% fetal bovine serum (FBS) and penicillin–streptomycin (100 U/mL) at 37 °C in an atmosphere containing 5% CO2. KOPN30 cells were obtained…

Dear CP2K users and developers: I am investigating the oxygen transport path in perovskite with CI-NEB. In order to consider DFT+U and generate “.model” file, I have to give up K-point and build a big cell with 250 atoms. I set 9 REPLICA. My computer doesn’t have enough memory(My computer…

Hello everyone,   Can anybody please help me with the following error in my error file? I have recently installed cp2k 8.2 version using intel-minimal.psmp arch file with intel 2018 compiler, gcc and fftw. Please guide me with job script and compilation.     forrtl: severe (174): SIGSEGV, segmentation fault…

Hi everyone, I have a single node server with two Xeon Gold 6154 CPU @ 3.00GHz, 18 cores each, 36 total, 72 threads. I have tested several NPROC_REP values in a series of vibrational analysis runs started with the following command:mpirun -np 72 –bind-to hwthread  cp2k.psmp -i cp2k.inp -o cp2k.out…

Hello everyone, I have a simple (100) copper slab (100 atoms, 4 layer==> see input.xyz); and I am trying to make the overall charge of my system equal to +1.39. Since the CHARGE tag only takes integers, I am trying to give partial charges to the atoms in the top…

Review . 2023 Mar 14;13:1147239. doi: 10.3389/fonc.2023.1147239. eCollection 2023. Affiliations Expand Affiliations 1 Department of Oncology, Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China. 2 Qingdao Cancer Institute, Qingdao, China. 3 School of Basic Medicine, Qingdao University, Qingdao, China. 4 Department of Pharmacology, School of Pharmacy, Qingdao University,…

FBXW7 is a member of the F-box protein family, which functions as the substrate recognition component of the SCF E3 ubiquitin ligase. FBXW7 is a main tumor suppressor due to its ability to control proteasome-mediated degradation of several oncoproteins such as c-Jun, c-Myc, Cyclin E1, mTOR, and Notch1-IC. FBXW7 inactivation…

Introduction Diabetic nephropathy (DN) is a type of severe complication of diabetes mellitus (DM) and is the main cause of chronic kidney disease (1). Various of mechanism are reported to be involved in the pathogenesis and development of DN, such as hyperglycemia, oxidative stress (2), mitochondrial dysfunction (3), endoplasmic reticulum…

Overview Product name Description Rabbit polyclonal to Fbxw7 Host species Rabbit Tested applications Species reactivity Reacts with: Mouse, Rat, Human Immunogen Recombinant full length protein…

Hi Janson   I would say that nothing «unexplainable” happened, just read the CP2k output. CP2K informs you that the “SCCS iteration cycle did not converge in 200 steps”. This happened already in the first SCF iteration step and thus everything thereafter becomes unreliable. The reasons for convergence failure can…

Dear cp2k developers and users, Recently I am trying to calculate pdos of a slab system and I am curious about if it is possible to obtain with ROKS instead of UKS scheme. However when I switched to ROKS, scf procedure ends normally but pdos calculation terminates with error segmentation…

Hello everyone, I have a list of differential genes (list1) and another list where I have the ID of the genes and the name (list2) and I want to name the genes from list1 taking the name from list2, how can I do this? I will appreciate your support, thanks….

Description Monoclonal Anti-FBXW7 antibody produced in mouse has been used in Western blotting and immunohistochemistry. F-box proteins are associated with various signaling pathways, such as nutrient sensing in yeast, conserved developmental pathways in plants and animals. These proteins mediate recognition of phosphorylated targets including Cyclin E, Myc, c-Jun, and Notch,…

Here is how you can get the structure from PubChem, read the SMILES into Avogadro2, do a MMFF94 (classical) optimization, and then a single-point energy calculation using NWChem (RHF, 6-31G*). The Avogadro2 Input builder will create a CP2K file if you prefer. For GROMACS, there is extensive documentation that includes…

Dear CP2K users, I’m struggling with convergence for bulk Fe, i.e. 3x3x3 supercell containing 54 Fe atoms. I wanted to simulate adsorption of different organic molecules on Fe(100) slab later, so this is my starting point. During GEO_OPT or CELL_OPT runs I sporadically encounter SCF issues like this: …    33 Broy./Diag….

Introduction Klebsiella pneumoniae (Kp; K. pneumoniae) is an important hospital and community-acquired pathogen that primarily causes pneumonia, urinary tract infections, bloodstream-associated infections, meningitis, and pyogenic liver abscess.1–3 Carbapenem antibiotics represent the most important treatment for Enterobacteriaceae; however, with the widespread use of such antibiotics, carbapenem-resistant K. pneumoniae (CRKP) is increasingly…

Hello, I am trying to sort a GFF file using the FASTA index output from samtools faidx. Both of my input files have content, but when I use the command below to sort my GFF, I get no output to the screen or file. bedtools sort -faidx F._oxysporum_f._sp._cubense_UK0001.fna.fai -i ../Mimps/F._oxysporum_f._sp._cubense_UK0001.fna_mimp_hits.gff…

The National Institute of Pharmaceutical Education & Research (NIPER), SAS Nagar is an autonomous Institute of National importance set up by the Government of India, Ministry of Chemicals & Fertilizers by an Act of Parliament, to impart higher education and undertake advanced research in the field of Pharmaceutical sciences, technology…

Introduction This tutorial is designed to illustrate how to relax the structureof a system (without changing the cell dimensions) using CP2K. Weuse the relaxation of a water (H\(_2\)O) molecule as an example. The example files are contained in geometry_optimisation.tgz that comes with this tutorial. The calculation was carried out with…

Organisation of the Pregap4 Manual Introduction Summary of the Files used and the Processing Steps Introduction to the Pregap4 User Interface Introduction to the Files to Process Window Introduction to the Configure Modules Window Introduction to the Textual Output Window Introduction to Running Pregap4 Pregap4 Menus Pregap4 File menu Pregap4…

The Staden Package Mini-Manual – Viewing Traces Using Trev For some types of sequencing project it is convenient to view and edit the chromatogram data prior to assembly into a gap4 database, and this is the function of the program trev. Trev displays the original trace data, its base calls…

F-box and WD repeat domain containing 7 (FBXW7) acts as a substrate receptor of SKP1-CUL1-F-box (SCF) E3 ubiquitin ligase and plays crucial roles in the regulation of several cellular processes, including cell growth, division, and differentiation, by targeting diverse key regulators for degradation. However, its role in regulating cellular senescence…

Using a permanently unlocked form of the plant enzyme MAX3, UC Davis researchers are exploring the mechanism by which the plant hormone strigoractone regulates a massive network of genes controlling plant growth and architecture. Credit: Nitzan Shabek/UC Davis As sessile organisms, plants have to continually adapt their growth and architecture…

Hallam, S. J., Goncharov, A., McEwen, J., Baran, R. & Jin, Y. Syd-1, a presynaptic protein with PDZ, C2 and rhoGAP-like domains specifies axon identity in C. elegans. Nat. Neurosci. 5, 1137–1146 (2002). CAS  PubMed  Google Scholar  Xu, Y. & Quinn, C. C. SYD-1 promotes multiple developmental steps leading to…

Dear CP2K users, I am performing geometry optimizations for Pt slab (fcc111) with one hydroxyl (OH) radical on top. First, the cell optimization of bulk Pt (fcc111) is performed and successfully converged (Pt_cellopt.xyz).  However, when I put one OH radical on Pt 111 to perform geometry optimization, I observed a…

Altman, B. J., Stine, Z. E. & Dang, C. V. From Krebs to clinic: glutamine metabolism to cancer therapy. Nat. Rev. Cancer 16, 619–634 (2016). CAS  Article  Google Scholar  Hensley, C. T., Wasti, A. T. & DeBerardinis, R. J. Glutamine and cancer: cell biology, physiology, and clinical opportunities. J. Clin….

Introduction Renal cell carcinoma (RCC) accounts for approximately 2–3% of all malignant tumors, and its prevalence is rising. Metastatic RCC accounts for 25–30% of all RCC cases, and has an exceedingly poor prognosis.1 In 2020, among approximately 430,000 newly discovered cases of RCC, 179,000 died.2 Clear cell renal cell carcinoma…

Hello All, I created a Ti2CO2 monolayer (MXene)  that I will attach as an xyz file. I want to run GEO_OPT on this structure with periodic boundary conditions only in the XY directions. In my output RESULTS file  the first SCF converges in 106 steps, but then the file is…

Dear cp2k users and experts, I want to use ASE as a job submission tool on supercomputer and further I plan to use ASE to perform Genetic Algorithm global optimization. However, I find for relatively large system containing more than 200 atoms (generated by GA, so it is always a…