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Showing 1 to 12 of 143 entries
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Controlling gene expression by DNA mechanics: emerging insights and challenges.

Biophysical reviews

Levens D, Baranello L, Kouzine F.
PMID: 28510225
Biophys Rev. 2016 Sep;8(3):259-268. doi: 10.1007/s12551-016-0216-8. Epub 2016 Aug 20.

Transcription initiation is a major control point for the precise regulation of gene expression. Our knowledge of this process has been mainly derived from protein-centric studies wherein cis-regulatory DNA sequences play a passive role, mainly in arranging the protein...

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Levens D, Baranello L, Kouzine F. Controlling gene expression by DNA mechanics: emerging insights and challenges. Biophys Rev. 2016;8(3):259-268doi: 10.1007/s12551-016-0216-8.
Levens, D., Baranello, L., & Kouzine, F. (2016). Controlling gene expression by DNA mechanics: emerging insights and challenges. Biophysical reviews, 8(3), 259-268. https://doi.org/10.1007/s12551-016-0216-8
Levens, David, et al. "Controlling gene expression by DNA mechanics: emerging insights and challenges." Biophysical reviews vol. 8,3 (2016): 259-268. doi: https://doi.org/10.1007/s12551-016-0216-8
Levens D, Baranello L, Kouzine F. Controlling gene expression by DNA mechanics: emerging insights and challenges. Biophys Rev. 2016 Sep;8(3):259-268. doi: 10.1007/s12551-016-0216-8. Epub 2016 Aug 20. PMID: 28510225; PMCID: PMC5425794.
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Revealing electronic open quantum systems with subsystem TDDFT.

The Journal of chemical physics

Krishtal A, Pavanello M.
PMID: 27036438
J Chem Phys. 2016 Mar 28;144(12):124118. doi: 10.1063/1.4944526.

Open quantum systems (OQSs) are perhaps the most realistic systems one can approach through simulations. In recent years, describing OQSs with Density Functional Theory (DFT) has been a prominent avenue of research with most approaches based on a density...

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Krishtal A, Pavanello M. Revealing electronic open quantum systems with subsystem TDDFT. J Chem Phys. 2016;144(12):124118doi: 10.1063/1.4944526.
Krishtal, A., & Pavanello, M. (2016). Revealing electronic open quantum systems with subsystem TDDFT. The Journal of chemical physics, 144(12), 124118. https://doi.org/10.1063/1.4944526
Krishtal, Alisa, and Pavanello, Michele. "Revealing electronic open quantum systems with subsystem TDDFT." The Journal of chemical physics vol. 144,12 (2016): 124118. doi: https://doi.org/10.1063/1.4944526
Krishtal A, Pavanello M. Revealing electronic open quantum systems with subsystem TDDFT. J Chem Phys. 2016 Mar 28;144(12):124118. doi: 10.1063/1.4944526. PMID: 27036438.
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Subsystem density-functional theory as an effective tool for modeling ground and excited states, their dynamics and many-body interactions.

Journal of physics. Condensed matter : an Institute of Physics journal

Krishtal A, Sinha D, Genova A, Pavanello M.
PMID: 25880118
J Phys Condens Matter. 2015 May 13;27(18):183202. doi: 10.1088/0953-8984/27/18/183202. Epub 2015 Apr 16.

Subsystem density-functional theory (DFT) is an emerging technique for calculating the electronic structure of complex molecular and condensed phase systems. In this topical review, we focus on some recent advances in this field related to the computation of condensed...

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Krishtal A, Sinha D, Genova A, et al. Subsystem density-functional theory as an effective tool for modeling ground and excited states, their dynamics and many-body interactions. J Phys Condens Matter. 2015;27(18):183202doi: 10.1088/0953-8984/27/18/183202.
Krishtal, A., Sinha, D., Genova, A., & Pavanello, M. (2015). Subsystem density-functional theory as an effective tool for modeling ground and excited states, their dynamics and many-body interactions. Journal of physics. Condensed matter : an Institute of Physics journal, 27(18), 183202. https://doi.org/10.1088/0953-8984/27/18/183202
Krishtal, Alisa, et al. "Subsystem density-functional theory as an effective tool for modeling ground and excited states, their dynamics and many-body interactions." Journal of physics. Condensed matter : an Institute of Physics journal vol. 27,18 (2015): 183202. doi: https://doi.org/10.1088/0953-8984/27/18/183202
Krishtal A, Sinha D, Genova A, Pavanello M. Subsystem density-functional theory as an effective tool for modeling ground and excited states, their dynamics and many-body interactions. J Phys Condens Matter. 2015 May 13;27(18):183202. doi: 10.1088/0953-8984/27/18/183202. Epub 2015 Apr 16. PMID: 25880118.
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High-Density Lipoprotein, Lecithin: Cholesterol Acyltransferase, and Atherosclerosis.

Endocrinology and metabolism (Seoul, Korea)

Ossoli A, Pavanello C, Calabresi L.
PMID: 27302716
Endocrinol Metab (Seoul). 2016 Jun;31(2):223-9. doi: 10.3803/EnM.2016.31.2.223. Epub 2016 Jun 10.

Epidemiological data clearly show the existence of a strong inverse correlation between plasma high-density lipoprotein cholesterol (HDL-C) concentrations and the incidence of coronary heart disease. This relation is explained by a number of atheroprotective properties of HDL, first of...

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Ossoli A, Pavanello C, Calabresi L. High-Density Lipoprotein, Lecithin: Cholesterol Acyltransferase, and Atherosclerosis. Endocrinol Metab (Seoul). 2016;31(2):223-9doi: 10.3803/EnM.2016.31.2.223.
Ossoli, A., Pavanello, C., & Calabresi, L. (2016). High-Density Lipoprotein, Lecithin: Cholesterol Acyltransferase, and Atherosclerosis. Endocrinology and metabolism (Seoul, Korea), 31(2), 223-9. https://doi.org/10.3803/EnM.2016.31.2.223
Ossoli, Alice, et al. "High-Density Lipoprotein, Lecithin: Cholesterol Acyltransferase, and Atherosclerosis." Endocrinology and metabolism (Seoul, Korea) vol. 31,2 (2016): 223-9. doi: https://doi.org/10.3803/EnM.2016.31.2.223
Ossoli A, Pavanello C, Calabresi L. High-Density Lipoprotein, Lecithin: Cholesterol Acyltransferase, and Atherosclerosis. Endocrinol Metab (Seoul). 2016 Jun;31(2):223-9. doi: 10.3803/EnM.2016.31.2.223. Epub 2016 Jun 10. PMID: 27302716; PMCID: PMC4923405.
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Inflammatory Long Pentraxin 3 is Associated with Leukocyte Telomere Length in Night-Shift Workers.

Frontiers in immunology

Pavanello S, Stendardo M, Mastrangelo G, Bonci M, Bottazzi B, Campisi M, Nardini M, Leone R, Mantovani A, Boschetto P.
PMID: 28536575
Front Immunol. 2017 May 09;8:516. doi: 10.3389/fimmu.2017.00516. eCollection 2017.

Aging is an emerging worldwide threat to public health, even in the workplace, as it links with risk of illness and death. Bewildered inflammatory responses and stressful conditions associate with age-related disorders. Additionally, circadian rhythm disruption, a critical health...

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Pavanello S, Stendardo M, Mastrangelo G, et al. Inflammatory Long Pentraxin 3 is Associated with Leukocyte Telomere Length in Night-Shift Workers. Front Immunol. 2017;8:516doi: 10.3389/fimmu.2017.00516.
Pavanello, S., Stendardo, M., Mastrangelo, G., Bonci, M., Bottazzi, B., Campisi, M., Nardini, M., Leone, R., Mantovani, A., & Boschetto, P. (2017). Inflammatory Long Pentraxin 3 is Associated with Leukocyte Telomere Length in Night-Shift Workers. Frontiers in immunology, 8516. https://doi.org/10.3389/fimmu.2017.00516
Pavanello, Sofia, et al. "Inflammatory Long Pentraxin 3 is Associated with Leukocyte Telomere Length in Night-Shift Workers." Frontiers in immunology vol. 8 (2017): 516. doi: https://doi.org/10.3389/fimmu.2017.00516
Pavanello S, Stendardo M, Mastrangelo G, Bonci M, Bottazzi B, Campisi M, Nardini M, Leone R, Mantovani A, Boschetto P. Inflammatory Long Pentraxin 3 is Associated with Leukocyte Telomere Length in Night-Shift Workers. Front Immunol. 2017 May 09;8:516. doi: 10.3389/fimmu.2017.00516. eCollection 2017. PMID: 28536575; PMCID: PMC5422482.
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Exploiting the locality of periodic subsystem density-functional theory: efficient sampling of the Brillouin zone.

Journal of physics. Condensed matter : an Institute of Physics journal

Genova A, Pavanello M.
PMID: 26596499
J Phys Condens Matter. 2015 Dec 16;27(49):495501. doi: 10.1088/0953-8984/27/49/495501. Epub 2015 Nov 24.

In order to approximately satisfy the Bloch theorem, simulations of complex materials involving periodic systems are made n(k) times more complex by the need to sample the first Brillouin zone at n(k) points. By combining ideas from Kohn-Sham density-functional...

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Genova A, Pavanello M. Exploiting the locality of periodic subsystem density-functional theory: efficient sampling of the Brillouin zone. J Phys Condens Matter. 2015;27(49):495501doi: 10.1088/0953-8984/27/49/495501.
Genova, A., & Pavanello, M. (2015). Exploiting the locality of periodic subsystem density-functional theory: efficient sampling of the Brillouin zone. Journal of physics. Condensed matter : an Institute of Physics journal, 27(49), 495501. https://doi.org/10.1088/0953-8984/27/49/495501
Genova, Alessandro, and Pavanello, Michele. "Exploiting the locality of periodic subsystem density-functional theory: efficient sampling of the Brillouin zone." Journal of physics. Condensed matter : an Institute of Physics journal vol. 27,49 (2015): 495501. doi: https://doi.org/10.1088/0953-8984/27/49/495501
Genova A, Pavanello M. Exploiting the locality of periodic subsystem density-functional theory: efficient sampling of the Brillouin zone. J Phys Condens Matter. 2015 Dec 16;27(49):495501. doi: 10.1088/0953-8984/27/49/495501. Epub 2015 Nov 24. PMID: 26596499.
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Communication: Visible line intensities of the triatomic hydrogen ion from experiment and theory.

The Journal of chemical physics

Petrignani A, Berg MH, Grussie F, Wolf A, Mizus II, Polyansky OL, Tennyson J, Zobov NF, Pavanello M, Adamowicz L.
PMID: 25554125
J Chem Phys. 2014 Dec 28;141(24):241104. doi: 10.1063/1.4904440.

The visible spectrum of H3(+) is studied using high-sensitivity action spectroscopy in a cryogenic radiofrequency multipole trap. Advances are made to measure the weak ro-vibrational transitions from the lowest rotational states of H3(+) up to high excitation energies providing...

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Petrignani A, Berg MH, Grussie F, et al. Communication: Visible line intensities of the triatomic hydrogen ion from experiment and theory. J Chem Phys. 2014;141(24):241104doi: 10.1063/1.4904440.
Petrignani, A., Berg, M. H., Grussie, F., Wolf, A., Mizus, I. I., Polyansky, O. L., Tennyson, J., Zobov, N. F., Pavanello, M., & Adamowicz, L. (2014). Communication: Visible line intensities of the triatomic hydrogen ion from experiment and theory. The Journal of chemical physics, 141(24), 241104. https://doi.org/10.1063/1.4904440
Petrignani, Annemieke, et al. "Communication: Visible line intensities of the triatomic hydrogen ion from experiment and theory." The Journal of chemical physics vol. 141,24 (2014): 241104. doi: https://doi.org/10.1063/1.4904440
Petrignani A, Berg MH, Grussie F, Wolf A, Mizus II, Polyansky OL, Tennyson J, Zobov NF, Pavanello M, Adamowicz L. Communication: Visible line intensities of the triatomic hydrogen ion from experiment and theory. J Chem Phys. 2014 Dec 28;141(24):241104. doi: 10.1063/1.4904440. PMID: 25554125.
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Exact kinetic energy enables accurate evaluation of weak interactions by the FDE-vdW method.

The Journal of chemical physics

Sinha D, Pavanello M.
PMID: 26328831
J Chem Phys. 2015 Aug 28;143(8):084120. doi: 10.1063/1.4928531.

The correlation energy of interaction is an elusive and sought-after interaction between molecular systems. By partitioning the response function of the system into subsystem contributions, the Frozen Density Embedding (FDE)-vdW method provides a computationally amenable nonlocal correlation functional based...

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Sinha D, Pavanello M. Exact kinetic energy enables accurate evaluation of weak interactions by the FDE-vdW method. J Chem Phys. 2015;143(8):084120doi: 10.1063/1.4928531.
Sinha, D., & Pavanello, M. (2015). Exact kinetic energy enables accurate evaluation of weak interactions by the FDE-vdW method. The Journal of chemical physics, 143(8), 084120. https://doi.org/10.1063/1.4928531
Sinha, Debalina, and Pavanello, Michele. "Exact kinetic energy enables accurate evaluation of weak interactions by the FDE-vdW method." The Journal of chemical physics vol. 143,8 (2015): 084120. doi: https://doi.org/10.1063/1.4928531
Sinha D, Pavanello M. Exact kinetic energy enables accurate evaluation of weak interactions by the FDE-vdW method. J Chem Phys. 2015 Aug 28;143(8):084120. doi: 10.1063/1.4928531. PMID: 26328831.
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Constitutional chromosomal events at 22q11 and 15q26 in a child with a pilocytic astrocytoma of the spinal cord.

Molecular cytogenetics

Mascelli S, Severino M, Raso A, Nozza P, Tassano E, Morana G, De Marco P, Merello E, Milanaccio C, Pavanello M, Rossi A, Cama A, Garrè ML, Capra V.
PMID: 24860619
Mol Cytogenet. 2014 May 15;7:31. doi: 10.1186/1755-8166-7-31. eCollection 2014.

We report on a 9-years-old patient with mild intellectual disability, facial dimorphisms, bilateral semicircular canal dysplasia, periventricular nodular heterotopias, bilateral hippocampal malrotation and abnormal cerebellar foliation, who developed mild motor impairment and gait disorder due to a pilocytic astrocytoma...

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Mascelli S, Severino M, Raso A, et al. Constitutional chromosomal events at 22q11 and 15q26 in a child with a pilocytic astrocytoma of the spinal cord. Mol Cytogenet. 2014;7:31doi: 10.1186/1755-8166-7-31.
Mascelli, S., Severino, M., Raso, A., Nozza, P., Tassano, E., Morana, G., De Marco, P., Merello, E., Milanaccio, C., Pavanello, M., Rossi, A., Cama, A., Garrè, M. L., & Capra, V. (2014). Constitutional chromosomal events at 22q11 and 15q26 in a child with a pilocytic astrocytoma of the spinal cord. Molecular cytogenetics, 731. https://doi.org/10.1186/1755-8166-7-31
Mascelli, Samantha, et al. "Constitutional chromosomal events at 22q11 and 15q26 in a child with a pilocytic astrocytoma of the spinal cord." Molecular cytogenetics vol. 7 (2014): 31. doi: https://doi.org/10.1186/1755-8166-7-31
Mascelli S, Severino M, Raso A, Nozza P, Tassano E, Morana G, De Marco P, Merello E, Milanaccio C, Pavanello M, Rossi A, Cama A, Garrè ML, Capra V. Constitutional chromosomal events at 22q11 and 15q26 in a child with a pilocytic astrocytoma of the spinal cord. Mol Cytogenet. 2014 May 15;7:31. doi: 10.1186/1755-8166-7-31. eCollection 2014. PMID: 24860619; PMCID: PMC4032172.
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Cytotoxic and mutagenic effects of anti- and syn-benzo[a]pyrene diol epoxide in human lymphocytes.

Toxicology in vitro : an international journal published in association with BIBRA

Zanesi N, Ferraro P, Pavanello S, Furlan D, Celotti L.
PMID: 20693099
Toxicol In Vitro. 1994 Dec;8(6):1269-75. doi: 10.1016/0887-2333(94)90120-1.

Cytotoxicity and mutagenicity were measured in human lymphocytes after treatment in vitro with anti- or syn-benzo[a]pyrene diolepoxide, two diastereoisomer metabolites of benzo[a]pyrene. These compounds were incubated with resting and cycling lymphocytes to determine the inhibition of cell proliferation induced...

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Zanesi N, Ferraro P, Pavanello S, et al. Cytotoxic and mutagenic effects of anti- and syn-benzo[a]pyrene diol epoxide in human lymphocytes. Toxicol In Vitro. 1994;8(6):1269-75doi: 10.1016/0887-2333(94)90120-1.
Zanesi, N., Ferraro, P., Pavanello, S., Furlan, D., & Celotti, L. (1994). Cytotoxic and mutagenic effects of anti- and syn-benzo[a]pyrene diol epoxide in human lymphocytes. Toxicology in vitro : an international journal published in association with BIBRA, 8(6), 1269-75. https://doi.org/10.1016/0887-2333(94)90120-1
Zanesi, N, et al. "Cytotoxic and mutagenic effects of anti- and syn-benzo[a]pyrene diol epoxide in human lymphocytes." Toxicology in vitro : an international journal published in association with BIBRA vol. 8,6 (1994): 1269-75. doi: https://doi.org/10.1016/0887-2333(94)90120-1
Zanesi N, Ferraro P, Pavanello S, Furlan D, Celotti L. Cytotoxic and mutagenic effects of anti- and syn-benzo[a]pyrene diol epoxide in human lymphocytes. Toxicol In Vitro. 1994 Dec;8(6):1269-75. doi: 10.1016/0887-2333(94)90120-1. PMID: 20693099.
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Accurate one-dimensional potential energy curve of the linear (H2)2 cluster.

The Journal of chemical physics

Tung WC, Pavanello M, Adamowicz L.
PMID: 20886923
J Chem Phys. 2010 Sep 28;133(12):124106. doi: 10.1063/1.3491029.

We present a sub-0.3 K accuracy, ground-state one-dimensional potential energy curve of the metastable linear configuration of the (H(2))(2) cluster calculated exclusively with explicitly correlated Gaussian functions with shifted centers. The H(2) internuclear distance is kept at the isolated...

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Tung WC, Pavanello M, Adamowicz L. Accurate one-dimensional potential energy curve of the linear (H2)2 cluster. J Chem Phys. 2010;133(12):124106doi: 10.1063/1.3491029.
Tung, W. C., Pavanello, M., & Adamowicz, L. (2010). Accurate one-dimensional potential energy curve of the linear (H2)2 cluster. The Journal of chemical physics, 133(12), 124106. https://doi.org/10.1063/1.3491029
Tung, Wei-Cheng, et al. "Accurate one-dimensional potential energy curve of the linear (H2)2 cluster." The Journal of chemical physics vol. 133,12 (2010): 124106. doi: https://doi.org/10.1063/1.3491029
Tung WC, Pavanello M, Adamowicz L. Accurate one-dimensional potential energy curve of the linear (H2)2 cluster. J Chem Phys. 2010 Sep 28;133(12):124106. doi: 10.1063/1.3491029. PMID: 20886923.
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Accurate potential energy curves for HeH+ isotopologues.

The Journal of chemical physics

Tung WC, Pavanello M, Adamowicz L.
PMID: 23126708
J Chem Phys. 2012 Oct 28;137(16):164305. doi: 10.1063/1.4759077.

New accurate ground-state potential energy curves (PEC) for the (4)HeH(+), (4)HeD(+), (3)HeH(+), and (3)HeD(+) isotopologues are calculated with 600 explicitly correlated Gaussian (ECG) functions with shifted centers in the range between R = 0.35 a(0) and 145 a(0). The...

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Tung WC, Pavanello M, Adamowicz L. Accurate potential energy curves for HeH+ isotopologues. J Chem Phys. 2012;137(16):164305doi: 10.1063/1.4759077.
Tung, W. C., Pavanello, M., & Adamowicz, L. (2012). Accurate potential energy curves for HeH+ isotopologues. The Journal of chemical physics, 137(16), 164305. https://doi.org/10.1063/1.4759077
Tung, Wei-Cheng, et al. "Accurate potential energy curves for HeH+ isotopologues." The Journal of chemical physics vol. 137,16 (2012): 164305. doi: https://doi.org/10.1063/1.4759077
Tung WC, Pavanello M, Adamowicz L. Accurate potential energy curves for HeH+ isotopologues. J Chem Phys. 2012 Oct 28;137(16):164305. doi: 10.1063/1.4759077. PMID: 23126708.
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Showing 1 to 12 of 143 entries