Advanced Search
Display options
Filter resources
Text Availability
Article type
Publication date
Species
Language
Sex
Age
Showing 1 to 12 of 329 entries
Sorted by: Best Match Show Resources per page
Concentration gradient driven molecular dynamics: a new method for simulations of membrane permeation and separation.

Chemical science

Ozcan A, Perego C, Salvalaglio M, Parrinello M, Yazaydin O.
PMID: 28966778
Chem Sci. 2017 May 01;8(5):3858-3865. doi: 10.1039/c6sc04978h. Epub 2017 Mar 20.

In this study, we introduce a new non-equilibrium molecular dynamics simulation method to perform simulations of concentration driven membrane permeation processes. The methodology is based on the application of a non-conservative bias force controlling the concentration of species at...

Cite
Ozcan A, Perego C, Salvalaglio M, et al. Concentration gradient driven molecular dynamics: a new method for simulations of membrane permeation and separation. Chem Sci. 2017;8(5):3858-3865doi: 10.1039/c6sc04978h.
Ozcan, A., Perego, C., Salvalaglio, M., Parrinello, M., & Yazaydin, O. (2017). Concentration gradient driven molecular dynamics: a new method for simulations of membrane permeation and separation. Chemical science, 8(5), 3858-3865. https://doi.org/10.1039/c6sc04978h
Ozcan, Aydin, et al. "Concentration gradient driven molecular dynamics: a new method for simulations of membrane permeation and separation." Chemical science vol. 8,5 (2017): 3858-3865. doi: https://doi.org/10.1039/c6sc04978h
Ozcan A, Perego C, Salvalaglio M, Parrinello M, Yazaydin O. Concentration gradient driven molecular dynamics: a new method for simulations of membrane permeation and separation. Chem Sci. 2017 May 01;8(5):3858-3865. doi: 10.1039/c6sc04978h. Epub 2017 Mar 20. PMID: 28966778; PMCID: PMC5578366.
Copy Download .nbib Format: NLM
Potential Role of Activating Transcription Factor 5 during Osteogenesis.

Stem cells international

Vicari L, Calabrese G, Forte S, Giuffrida R, Colarossi C, Parrinello NL, Memeo L.
PMID: 26770207
Stem Cells Int. 2016;2016:5282185. doi: 10.1155/2016/5282185. Epub 2015 Dec 06.

Human adipose-derived stem cells are an abundant population of stem cells readily isolated from human adipose tissue that can differentiate into connective tissue lineages including bone, cartilage, fat, and muscle. Activating transcription factor 5 is a transcription factor of...

Cite
Vicari L, Calabrese G, Forte S, et al. Potential Role of Activating Transcription Factor 5 during Osteogenesis. Stem Cells Int. 2015;2016:5282185doi: 10.1155/2016/5282185.
Vicari, L., Calabrese, G., Forte, S., Giuffrida, R., Colarossi, C., Parrinello, N. L., & Memeo, L. (2016). Potential Role of Activating Transcription Factor 5 during Osteogenesis. Stem cells international, 20165282185. https://doi.org/10.1155/2016/5282185
Vicari, Luisa, et al. "Potential Role of Activating Transcription Factor 5 during Osteogenesis." Stem cells international vol. 2016 (2016): 5282185. doi: https://doi.org/10.1155/2016/5282185
Vicari L, Calabrese G, Forte S, Giuffrida R, Colarossi C, Parrinello NL, Memeo L. Potential Role of Activating Transcription Factor 5 during Osteogenesis. Stem Cells Int. 2016;2016:5282185. doi: 10.1155/2016/5282185. Epub 2015 Dec 06. PMID: 26770207; PMCID: PMC4684884.
Copy Download .nbib Format: NLM
Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model.

Proceedings of the National Academy of Sciences of the United States of America

Invernizzi M, Valsson O, Parrinello M.
PMID: 28292890
Proc Natl Acad Sci U S A. 2017 Mar 28;114(13):3370-3374. doi: 10.1073/pnas.1618455114. Epub 2017 Mar 14.

A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often...

Cite
Invernizzi M, Valsson O, Parrinello M. Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model. Proc Natl Acad Sci U S A. 2017;114(13):3370-3374doi: 10.1073/pnas.1618455114.
Invernizzi, M., Valsson, O., & Parrinello, M. (2017). Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model. Proceedings of the National Academy of Sciences of the United States of America, 114(13), 3370-3374. https://doi.org/10.1073/pnas.1618455114
Invernizzi, Michele, et al. "Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model." Proceedings of the National Academy of Sciences of the United States of America vol. 114,13 (2017): 3370-3374. doi: https://doi.org/10.1073/pnas.1618455114
Invernizzi M, Valsson O, Parrinello M. Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model. Proc Natl Acad Sci U S A. 2017 Mar 28;114(13):3370-3374. doi: 10.1073/pnas.1618455114. Epub 2017 Mar 14. PMID: 28292890; PMCID: PMC5380034.
Copy Download .nbib Format: NLM
Immunological deregulation in classic hodgkin lymphoma.

Mediterranean journal of hematology and infectious diseases

Romano A, Vetro C, Caocci G, Greco M, Parrinello NL, Di Raimondo F, La Nasa G.
PMID: 24959336
Mediterr J Hematol Infect Dis. 2014 Jun 01;6(1):e2014039. doi: 10.4084/MJHID.2014.039. eCollection 2014.

Classic Hodgkin Lymphoma (cHL) has a unique histology since only a few neoplastic cells are surrounded by inflammatory accessory cells that in the last years have emerged as crucial players in sustaining the course of disease. In addition, recent...

Cite
Romano A, Vetro C, Caocci G, et al. Immunological deregulation in classic hodgkin lymphoma. Mediterr J Hematol Infect Dis. 2014;6(1):e2014039doi: 10.4084/MJHID.2014.039.
Romano, A., Vetro, C., Caocci, G., Greco, M., Parrinello, N. L., Di Raimondo, F., & La Nasa, G. (2014). Immunological deregulation in classic hodgkin lymphoma. Mediterranean journal of hematology and infectious diseases, 6(1), e2014039. https://doi.org/10.4084/MJHID.2014.039
Romano, Alessandra, et al. "Immunological deregulation in classic hodgkin lymphoma." Mediterranean journal of hematology and infectious diseases vol. 6,1 (2014): e2014039. doi: https://doi.org/10.4084/MJHID.2014.039
Romano A, Vetro C, Caocci G, Greco M, Parrinello NL, Di Raimondo F, La Nasa G. Immunological deregulation in classic hodgkin lymphoma. Mediterr J Hematol Infect Dis. 2014 Jun 01;6(1):e2014039. doi: 10.4084/MJHID.2014.039. eCollection 2014. PMID: 24959336; PMCID: PMC4063611.
Copy Download .nbib Format: NLM
Transient Polymorphism in NaCl.

Journal of chemical theory and computation

Giberti F, Tribello GA, Parrinello M.
PMID: 26583849
J Chem Theory Comput. 2013 Jun 11;9(6):2526-30. doi: 10.1021/ct4002027. Epub 2013 May 08.

We introduce a new collective variable (CV) that can be used to increase the frequency with which nucleation events are observed in biased atomistic simulations. This CV forces the ions to aggregate into clusters but does not force the...

Cite
Giberti F, Tribello GA, Parrinello M. Transient Polymorphism in NaCl. J Chem Theory Comput. 2013;9(6):2526-30doi: 10.1021/ct4002027.
Giberti, F., Tribello, G. A., & Parrinello, M. (2013). Transient Polymorphism in NaCl. Journal of chemical theory and computation, 9(6), 2526-30. https://doi.org/10.1021/ct4002027
Giberti, Federico, et al. "Transient Polymorphism in NaCl." Journal of chemical theory and computation vol. 9,6 (2013): 2526-30. doi: https://doi.org/10.1021/ct4002027
Giberti F, Tribello GA, Parrinello M. Transient Polymorphism in NaCl. J Chem Theory Comput. 2013 Jun 11;9(6):2526-30. doi: 10.1021/ct4002027. Epub 2013 May 08. PMID: 26583849.
Copy Download .nbib Format: NLM
Thermodynamical Description of a Quasi-First-Order Phase Transition from the Well-Tempered Ensemble.

Journal of chemical theory and computation

Valsson O, Parrinello M.
PMID: 26592265
J Chem Theory Comput. 2013 Dec 10;9(12):5267-76. doi: 10.1021/ct400859f. Epub 2013 Nov 21.

We explore the performance of the well-tempered ensemble combined with parallel tempering (PT-WTE) in obtaining a thermodynamical description of a given molecular system. We carefully explain the theoretical procedure employed to extract all the relevant thermodynamical quantities from a...

Cite
Valsson O, Parrinello M. Thermodynamical Description of a Quasi-First-Order Phase Transition from the Well-Tempered Ensemble. J Chem Theory Comput. 2013;9(12):5267-76doi: 10.1021/ct400859f.
Valsson, O., & Parrinello, M. (2013). Thermodynamical Description of a Quasi-First-Order Phase Transition from the Well-Tempered Ensemble. Journal of chemical theory and computation, 9(12), 5267-76. https://doi.org/10.1021/ct400859f
Valsson, Omar, and Parrinello, Michele. "Thermodynamical Description of a Quasi-First-Order Phase Transition from the Well-Tempered Ensemble." Journal of chemical theory and computation vol. 9,12 (2013): 5267-76. doi: https://doi.org/10.1021/ct400859f
Valsson O, Parrinello M. Thermodynamical Description of a Quasi-First-Order Phase Transition from the Well-Tempered Ensemble. J Chem Theory Comput. 2013 Dec 10;9(12):5267-76. doi: 10.1021/ct400859f. Epub 2013 Nov 21. PMID: 26592265.
Copy Download .nbib Format: NLM
"We are what we eat!" Invasive intestinal mucormycosis: A case report and review of the literature.

Medical mycology case reports

Martinello M, Nelson A, Bignold L, Shaw D.
PMID: 24371738
Med Mycol Case Rep. 2012 Aug 04;1(1):52-5. doi: 10.1016/j.mmcr.2012.07.003. eCollection 2012.

Gastrointestinal mucormycosis is an uncommon, life-threatening, angioinvasive infection with only one previous report of disease involving the jejunum. We present a case of invasive jejunal mucormycosis and review the literature, highlighting the rare clinical presentation and the value of...

Cite
Martinello M, Nelson A, Bignold L, et al. "We are what we eat!" Invasive intestinal mucormycosis: A case report and review of the literature. Med Mycol Case Rep. 2012;1(1):52-5doi: 10.1016/j.mmcr.2012.07.003.
Martinello, M., Nelson, A., Bignold, L., & Shaw, D. (2012). "We are what we eat!" Invasive intestinal mucormycosis: A case report and review of the literature. Medical mycology case reports, 1(1), 52-5. https://doi.org/10.1016/j.mmcr.2012.07.003
Martinello, Marianne, et al. ""We are what we eat!" Invasive intestinal mucormycosis: A case report and review of the literature." Medical mycology case reports vol. 1,1 (2012): 52-5. doi: https://doi.org/10.1016/j.mmcr.2012.07.003
Martinello M, Nelson A, Bignold L, Shaw D. "We are what we eat!" Invasive intestinal mucormycosis: A case report and review of the literature. Med Mycol Case Rep. 2012 Aug 04;1(1):52-5. doi: 10.1016/j.mmcr.2012.07.003. eCollection 2012. PMID: 24371738; PMCID: PMC3855875.
Copy Download .nbib Format: NLM
Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA.

Journal of chemical theory and computation

Do TN, Ippoliti E, Carloni P, Varani G, Parrinello M.
PMID: 26596616
J Chem Theory Comput. 2012 Feb 14;8(2):688-94. doi: 10.1021/ct2005769. Epub 2012 Jan 20.

Binding of proteins and small molecules to RNA involves many electrostatic interactions, which may alter the distribution of ions around the RNA molecule. Here, we use molecular dynamics simulations to investigate how binding of a cyclic peptide mimic of...

Cite
Do TN, Ippoliti E, Carloni P, et al. Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA. J Chem Theory Comput. 2012;8(2):688-94doi: 10.1021/ct2005769.
Do, T. N., Ippoliti, E., Carloni, P., Varani, G., & Parrinello, M. (2012). Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA. Journal of chemical theory and computation, 8(2), 688-94. https://doi.org/10.1021/ct2005769
Do, Trang N, et al. "Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA." Journal of chemical theory and computation vol. 8,2 (2012): 688-94. doi: https://doi.org/10.1021/ct2005769
Do TN, Ippoliti E, Carloni P, Varani G, Parrinello M. Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA. J Chem Theory Comput. 2012 Feb 14;8(2):688-94. doi: 10.1021/ct2005769. Epub 2012 Jan 20. PMID: 26596616.
Copy Download .nbib Format: NLM
Replica Temperatures for Uniform Exchange and Efficient Roundtrip Times in Explicit Solvent Parallel Tempering Simulations.

Journal of chemical theory and computation

Prakash MK, Barducci A, Parrinello M.
PMID: 26606473
J Chem Theory Comput. 2011 Jul 12;7(7):2025-7. doi: 10.1021/ct200208h. Epub 2011 Jun 22.

The efficiency of parallel tempering simulations is greatly influenced by the distribution of replica temperatures. In explicit solvent biomolecular simulations, where the total energy is dominated by the solvent, specific heat is usually assumed to be constant. From this,...

Cite
Prakash MK, Barducci A, Parrinello M. Replica Temperatures for Uniform Exchange and Efficient Roundtrip Times in Explicit Solvent Parallel Tempering Simulations. J Chem Theory Comput. 2011;7(7):2025-7doi: 10.1021/ct200208h.
Prakash, M. K., Barducci, A., & Parrinello, M. (2011). Replica Temperatures for Uniform Exchange and Efficient Roundtrip Times in Explicit Solvent Parallel Tempering Simulations. Journal of chemical theory and computation, 7(7), 2025-7. https://doi.org/10.1021/ct200208h
Prakash, Meher K, et al. "Replica Temperatures for Uniform Exchange and Efficient Roundtrip Times in Explicit Solvent Parallel Tempering Simulations." Journal of chemical theory and computation vol. 7,7 (2011): 2025-7. doi: https://doi.org/10.1021/ct200208h
Prakash MK, Barducci A, Parrinello M. Replica Temperatures for Uniform Exchange and Efficient Roundtrip Times in Explicit Solvent Parallel Tempering Simulations. J Chem Theory Comput. 2011 Jul 12;7(7):2025-7. doi: 10.1021/ct200208h. Epub 2011 Jun 22. PMID: 26606473.
Copy Download .nbib Format: NLM
RNA-seq de novo Assembly Reveals Differential Gene Expression in Glossina palpalis gambiensis Infected with Trypanosoma brucei gambiense vs. Non-Infected and Self-Cured Flies.

Frontiers in microbiology

Hamidou Soumana I, Klopp C, Ravel S, Nabihoudine I, Tchicaya B, Parrinello H, Abate L, Rialle S, Geiger A.
PMID: 26617594
Front Microbiol. 2015 Nov 13;6:1259. doi: 10.3389/fmicb.2015.01259. eCollection 2015.

Trypanosoma brucei gambiense (Tbg), causing the sleeping sickness chronic form, completes its developmental cycle within the tsetse fly vector Glossina palpalis gambiensis (Gpg) before its transmission to humans. Within the framework of an anti-vector disease control strategy, a global...

Cite
Hamidou Soumana I, Klopp C, Ravel S, et al. RNA-seq de novo Assembly Reveals Differential Gene Expression in Glossina palpalis gambiensis Infected with Trypanosoma brucei gambiense vs. Non-Infected and Self-Cured Flies. Front Microbiol. 2015;6:1259doi: 10.3389/fmicb.2015.01259.
Hamidou Soumana, I., Klopp, C., Ravel, S., Nabihoudine, I., Tchicaya, B., Parrinello, H., Abate, L., Rialle, S., & Geiger, A. (2015). RNA-seq de novo Assembly Reveals Differential Gene Expression in Glossina palpalis gambiensis Infected with Trypanosoma brucei gambiense vs. Non-Infected and Self-Cured Flies. Frontiers in microbiology, 61259. https://doi.org/10.3389/fmicb.2015.01259
Hamidou Soumana, Illiassou, et al. "RNA-seq de novo Assembly Reveals Differential Gene Expression in Glossina palpalis gambiensis Infected with Trypanosoma brucei gambiense vs. Non-Infected and Self-Cured Flies." Frontiers in microbiology vol. 6 (2015): 1259. doi: https://doi.org/10.3389/fmicb.2015.01259
Hamidou Soumana I, Klopp C, Ravel S, Nabihoudine I, Tchicaya B, Parrinello H, Abate L, Rialle S, Geiger A. RNA-seq de novo Assembly Reveals Differential Gene Expression in Glossina palpalis gambiensis Infected with Trypanosoma brucei gambiense vs. Non-Infected and Self-Cured Flies. Front Microbiol. 2015 Nov 13;6:1259. doi: 10.3389/fmicb.2015.01259. eCollection 2015. PMID: 26617594; PMCID: PMC4643127.
Copy Download .nbib Format: NLM
Combustion chemistry via metadynamics: benzyl decomposition revisited.

The journal of physical chemistry. A

Polino D, Parrinello M.
PMID: 25587630
J Phys Chem A. 2015 Feb 12;119(6):978-89. doi: 10.1021/jp5118807. Epub 2015 Jan 28.

Large polycyclic aromatic hydrocarbons (PAHs) are thought to be responsible for the formation of soot particles in combustion processes. However, there are still uncertainties on the course that leads small molecules to form PAHs. This is largely due to...

Cite
Polino D, Parrinello M. Combustion chemistry via metadynamics: benzyl decomposition revisited. J Phys Chem A. 2015;119(6):978-89doi: 10.1021/jp5118807.
Polino, D., & Parrinello, M. (2015). Combustion chemistry via metadynamics: benzyl decomposition revisited. The journal of physical chemistry. A, 119(6), 978-89. https://doi.org/10.1021/jp5118807
Polino, Daniela, and Parrinello, Michele. "Combustion chemistry via metadynamics: benzyl decomposition revisited." The journal of physical chemistry. A vol. 119,6 (2015): 978-89. doi: https://doi.org/10.1021/jp5118807
Polino D, Parrinello M. Combustion chemistry via metadynamics: benzyl decomposition revisited. J Phys Chem A. 2015 Feb 12;119(6):978-89. doi: 10.1021/jp5118807. Epub 2015 Jan 28. PMID: 25587630.
Copy Download .nbib Format: NLM
Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint.

Annual review of physical chemistry

Valsson O, Tiwary P, Parrinello M.
PMID: 26980304
Annu Rev Phys Chem. 2016 May 27;67:159-84. doi: 10.1146/annurev-physchem-040215-112229. Epub 2016 Mar 10.

Atomistic simulations play a central role in many fields of science. However, their usefulness is often limited by the fact that many systems are characterized by several metastable states separated by high barriers, leading to kinetic bottlenecks. Transitions between...

Cite
Valsson O, Tiwary P, Parrinello M. Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint. Annu Rev Phys Chem. 2016;67:159-84doi: 10.1146/annurev-physchem-040215-112229.
Valsson, O., Tiwary, P., & Parrinello, M. (2016). Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint. Annual review of physical chemistry, 67159-84. https://doi.org/10.1146/annurev-physchem-040215-112229
Valsson, Omar, et al. "Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint." Annual review of physical chemistry vol. 67 (2016): 159-84. doi: https://doi.org/10.1146/annurev-physchem-040215-112229
Valsson O, Tiwary P, Parrinello M. Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint. Annu Rev Phys Chem. 2016 May 27;67:159-84. doi: 10.1146/annurev-physchem-040215-112229. Epub 2016 Mar 10. PMID: 26980304.
Copy Download .nbib Format: NLM
Showing 1 to 12 of 329 entries